Format Overview For Developers

Python implementation

Linkml generates a datamodel file with all classes: https://github.com/PlasmoGenEpi/portable-micorhaplotype-object/blob/main/src/plasmo_tar_amp_schema/datamodel/plasmo_tar_amp_schema.py

Tools

Started development of a tool called pmotools. Python implementation can be found here: https://github.com/PlasmoGenEpi/pmotools-python/tree/develop

Format overview

Below is an overview of the entire format currently in development which is under active development and optimization. Please send questions to info@plasmogenepi.org

PortableMicrohaplotypeObject

https://plasmogenepi.github.io/portable-microhaplotype-object/PortableMicrohaplotypeObject/

Required

library_sample_info (type=list of LibrarySampleInfo)
- a list of libraries of all the seq/amp of the specimens within this project
specimen_info (type=list of SpecimenInfo)
- a list of all the specimens within this project
sequencing_info (type=list of SequencingInfo)
- a list of sequencing info for this project
panel_info (type=list of PanelInfo)
- a list of info on the panels
target_info (type=list of TargetInfo)
- a list of info on the targets
targeted_genomes (type=list of GenomeInfo)
- a list of genomes that the targets in TargetInfo refer to
representative_microhaplotypes (type=RepresentativeMicrohaplotypes)
- a list of the information on the representative microhaplotypes
bioinformatics_methods_info (type=list of BioinformaticsMethodInfo)
- the bioinformatics pipeline/methods used to generated the amplicon analysis for this project
bioinformatics_run_info (type=list of BioinformaticsRunInfo)
- the runtime info for the bioinformatics pipeline used to generated the amplicon analysis for this project
detected_microhaplotypes (type=list of DetectedMicrohaplotypes)
- the microhaplotypes detected in this projects
project_info (type=list of ProjectInfo)
- the information about the projects stored in this PMO
pmo_header (type=PmoHeader)
- the PMO information for this file including version etc

Optional

read_counts_by_stage (type=list of ReadCountsByStage)
- the read counts for different stages of the pipeline

Example

Code

BioMethod

https://plasmogenepi.github.io/portable-microhaplotype-object/BioMethod/
Show BioMethod fields

Required

program_version (type=string)
- the version of generation method, should be in the format of v[MAJOR].[MINOR].[PATCH]
program (type=string)
- name of the program used for this portion of the pipeline

Optional

additional_argument (type=list of string)
- any additional arguments that differ from the default
program_description (type=string)
- a short description of what this method does
program_url (type=string)
- a url pointing to code base of a program, e.g. a github link

Example

Code

BioinformaticsMethodInfo

https://plasmogenepi.github.io/portable-microhaplotype-object/BioinformaticsMethodInfo/
Show BioinformaticsMethodInfo fields

Required

demultiplexing_method (type=BioMethod)
- the demultiplexing method used to separate raw reads from barcodes and primer targets
denoising_method (type=BioMethod)
- the method used to de-noise and/or cluster the raw reads

Optional

additional_methods (type=list of BioMethod)
- any additional methods used to analyze the data
bioinformatics_method_name (type=string)
- name of the collection of methods is called, e.g. pipeline

Example

Code

BioinformaticsRunInfo

https://plasmogenepi.github.io/portable-microhaplotype-object/BioinformaticsRunInfo/
Show BioinformaticsRunInfo fields

Required

bioinformatics_methods_id (type=integer)
- the index into the bioinformatics_methods_info list
bioinformatics_run_name (type=string)
- a name to for this run, needs to be unique to each run

Optional

run_date (type=string)
- the date when the run was done, should be YYYY-MM-DD

Example

Code

DetectedMicrohaplotypes

https://plasmogenepi.github.io/portable-microhaplotype-object/DetectedMicrohaplotypes/
Show DetectedMicrohaplotypes fields

Required

bioinformatics_run_id (type=integer)
- the index into bioinformatics_run_info list
library_samples (type=list of DetectedMicrohaplotypesForSample)
- a list of the microhaplotypes detected for a sample by targets

Example

Code

DetectedMicrohaplotypesForSample

https://plasmogenepi.github.io/portable-microhaplotype-object/DetectedMicrohaplotypesForSample/
Show DetectedMicrohaplotypesForSample fields

Required

library_sample_id (type=integer)
- the index into the library_sample_info list
target_results (type=list of DetectedMicrohaplotypesForTarget)
- a list of the microhaplotypes detected for a list of targets

Example

Code

DetectedMicrohaplotypesForTarget

https://plasmogenepi.github.io/portable-microhaplotype-object/DetectedMicrohaplotypesForTarget/
Show DetectedMicrohaplotypesForTarget fields

Required

mhaps_target_id (type=integer)
- the index for a target in the representative_microhaplotypes list
mhaps (type=list of MicrohaplotypeForTarget)
- a list of the microhaplotypes detected for this target

Example

Code

GenomeInfo

https://plasmogenepi.github.io/portable-microhaplotype-object/GenomeInfo/
Show GenomeInfo fields

Required

name (type=string)
- name of the genome
genome_version (type=string)
- the genome version
taxon_id (type= list of integer)
- the NCBI taxonomy number, can be a list of values
url (type=string)
- a link to the where this genome file could be downloaded

Optional

chromosomes (type=list of string)
- a list of chromosomes found within this genome
gff_url (type=string)
- a link to the where this genome’s annotation file could be downloaded

Example

Code

GenomicLocation

https://plasmogenepi.github.io/portable-microhaplotype-object/GenomicLocation/
Show GenomicLocation fields

Required

genome_id (type=integer)
- the index to the genome in the targeted_genomes list that this location refers to
chrom (type=string)
- the chromosome name
start (type=integer)
- the start of the location, 0-based positioning
end (type=integer)
- the end of the location, 0-based positioning

Optional

alt_seq (type=string)
- a possible alternative sequence of this genomic location
ref_seq (type=string)
- the reference sequence of this genomic location
strand (type=string)
- which strand the location is, either + for plus strand or - for negative strand

Example

Code

LibrarySampleInfo

https://plasmogenepi.github.io/portable-microhaplotype-object/LibrarySampleInfo/
Show LibrarySampleInfo fields

Required

sequencing_info_id (type=integer)
- the index into the sequencing_info list
specimen_id (type=integer)
- the index into the specimen_info list
panel_id (type=integer)
- the index into the panel_info list
library_sample_name (type=string)
- a unique identifier for this sequence/amplification run on a specimen_name

Optional

alternate_identifiers (type=list of string)
- a list of optional alternative names
experiment_accession (type=string)
- ERA/SRA experiment accession number for the sample if it was submitted
fastqs_loc (type=string)
- the location (url or filename path) of the fastqs for a library run
library_prep_plate_info (type=PlateInfo)
- plate location of where library was prepared for sequencing
qpcr_parasite_density_info (type=list of ParasiteDensity)
- qpcr parasite density measurement for this extracted sample
run_accession (type=string)
- ERA/SRA run accession number for the sample if it was submitted

Example

Code

MarkerOfInterest

https://plasmogenepi.github.io/portable-microhaplotype-object/MarkerOfInterest/
Show MarkerOfInterest fields

Required

marker_location (type=GenomicLocation)
- the genomic location

Optional

associations (type=list of string)
- a list of associations with this marker, e.g. SP resistance, etc

Example

Code

MaskingInfo

https://plasmogenepi.github.io/portable-microhaplotype-object/MaskingInfo/
Show MaskingInfo fields

Required

seq_start (type=integer)
- the start of the masking
seq_segment_size (type=integer)
- the size of the masking
replacement_size (type=integer)
- the size of replacement mask

Optional

masking_generation_description (type=string)
- a description of how the masking information was generated

Example

Code

MicrohaplotypeForTarget

https://plasmogenepi.github.io/portable-microhaplotype-object/MicrohaplotypeForTarget/
Show MicrohaplotypeForTarget fields

Required

mhap_id (type=integer)
- the index for a microhaplotype for a target in the representative_microhaplotypes list, e.g. representative_microhaplotypes[mhaps_target_id][mhap_id]
reads (type=integer)
- the read count associated with this microhaplotype

Optional

umis (type=integer)
- the unique molecular identifier (umi) count associated with this microhaplotype

Example

Code

PanelInfo

https://plasmogenepi.github.io/portable-microhaplotype-object/PanelInfo/
Show PanelInfo fields

Required

reactions (type=list of ReactionInfo)
- a list of 1 or more reactions that this panel contains, each reactions list the targets that were amplified in that reaction, e.g. pool1, pool2
panel_name (type=string)
- a name for the panel

Example

Code

ParasiteDensity

https://plasmogenepi.github.io/portable-microhaplotype-object/ParasiteDensity/
Show ParasiteDensity fields

Required

parasite_density_method (type=string)
- the method of how this density was obtained
parasite_density (type=number)
- the density in microliters

Optional

date_measured (type=string)
- the date the qpcr was performed, can be YYYY, YYYY-MM, or YYYY-MM-DD
density_method_comments (type=string)
- additional comments about how the density was performed

Example

Code

PlateInfo

https://plasmogenepi.github.io/portable-microhaplotype-object/PlateInfo/
Show PlateInfo fields

Required

Optional

plate_col (type=integer)
- the column the specimen was in
plate_name (type=string)
- a name of plate the specimen was in
plate_row (type=string)
- the row the specimen was in

Example

Code

PmoGenerationMethod

https://plasmogenepi.github.io/portable-microhaplotype-object/PmoGenerationMethod/
Show PmoGenerationMethod fields

Required

program_version (type=string)
- the version of generation method, should be in the format of v[MAJOR].[MINOR].[PATCH]
program_name (type=string)
- the name of the program

Example

Code

PmoHeader

https://plasmogenepi.github.io/portable-microhaplotype-object/PmoHeader/
Show PmoHeader fields

Required

pmo_version (type=string)
- the version of the PMO file, should be in the format of v[MAJOR].[MINOR].[PATCH]

Optional

creation_date (type=string)
- the date of when the PMO file was created or modified, should be YYYY-MM-DD
generation_method (type=PmoGenerationMethod)
- the generation method to create this PMO

Example

Code

PrimerInfo

https://plasmogenepi.github.io/portable-microhaplotype-object/PrimerInfo/
Show PrimerInfo fields

Required

seq (type=string)
- the DNA sequence

Optional

location (type=GenomicLocation)
- what the intended genomic location of the primer is

Example

Code

ProjectInfo

https://plasmogenepi.github.io/portable-microhaplotype-object/ProjectInfo/
Show ProjectInfo fields

Required

project_name (type=string)
- a name for the project, should be unique if multiple projects listed
project_description (type=string)
- a short description of the project

Optional

BioProject_accession (type=string)
- an SRA bioproject accession e.g. PRJNA33823
project_collector_chief_scientist (type=string)
- can be collection of names separated by a semicolon if multiple people involved or can just be the name of the primary person managing the specimen
project_contributors (type=list of string)
- a list of collaborators who contributed to this project
project_type (type=string)
- the type of project conducted, e.g. TES vs surveillance vs transmission

Example

Code

ProteinVariant

https://plasmogenepi.github.io/portable-microhaplotype-object/ProteinVariant/
Show ProteinVariant fields

Required

protein_location (type=GenomicLocation)
- the position within the protein, the chromosome in this case would be the transcript name

Optional

alternative_gene_name (type=string)
- an alternative gene name
codon_genomic_location (type=GenomicLocation)
- the position within the genomic sequence of the codon
gene_name (type=string)
- an identifier of the gene, if any, is being covered with this targeted

Example

Code

Pseudocigar

https://plasmogenepi.github.io/portable-microhaplotype-object/Pseudocigar/
Show Pseudocigar fields

Required

pseudocigar_seq (type=string)
- the pseudocigar itself
ref_loc (type=GenomicLocation)
- the genomic location the pseudocigar is in reference to

Optional

pseudocigar_generation_description (type=string)
- a description of how the pseudocigar information was generated

Example

Code

ReactionInfo

https://plasmogenepi.github.io/portable-microhaplotype-object/ReactionInfo/
Show ReactionInfo fields

Required

panel_targets (type= list of integer)
- a list of the target indexes in the target_info list
reaction_name (type=string)
- a name for this reaction

Example

Code

ReadCountsByStage

https://plasmogenepi.github.io/portable-microhaplotype-object/ReadCountsByStage/
Show ReadCountsByStage fields

Required

bioinformatics_run_id (type=integer)
- the index into bioinformatics_run_info list
read_counts_by_library_sample_by_stage (type=list of ReadCountsByStageForLibrarySample)
- a list by library_sample for the counts at each stage

Example

Code

ReadCountsByStageForLibrarySample

https://plasmogenepi.github.io/portable-microhaplotype-object/ReadCountsByStageForLibrarySample/
Show ReadCountsByStageForLibrarySample fields

Required

library_sample_id (type=integer)
- the index into the library_sample_info list
total_raw_count (type=integer)
- the raw counts off the sequencing machine that a sample began with

Optional

read_counts_for_targets (type=list of ReadCountsByStageForTarget)
- a list of counts by stage for a target

Example

Code

ReadCountsByStageForTarget

https://plasmogenepi.github.io/portable-microhaplotype-object/ReadCountsByStageForTarget/
Show ReadCountsByStageForTarget fields

Required

target_id (type=integer)
- the index into the target_info list
stages (type=list of StageReadCounts)
- the read counts by each stage

Example

Code

RepresentativeMicrohaplotype

https://plasmogenepi.github.io/portable-microhaplotype-object/RepresentativeMicrohaplotype/
Show RepresentativeMicrohaplotype fields

Required

seq (type=string)
- the DNA sequence

Optional

alt_annotations (type=list of string)
- a list of additional annotations associated with this microhaplotype, e.g. wildtype
associated_protein_variants (type=list of ProteinVariant)
- a list of associated protein variants with this haplotype, e.g. amino acid changes/INDELS
associated_seq_variants (type=list of GenomicLocation)
- a list of associated sequence variants with this haplotype, e.g. SNPS, indels
masking (type=list of MaskingInfo)
- masking info for the sequence
microhaplotype_name (type=string)
- an optional name for this microhaplotype
pseudocigar (type=Pseudocigar)
- the pseudocigar of the haplotype
quality (type=string)
- the ansi fastq per base quality score for this sequence, this is optional

Example

Code

RepresentativeMicrohaplotypes

https://plasmogenepi.github.io/portable-microhaplotype-object/RepresentativeMicrohaplotypes/
Show RepresentativeMicrohaplotypes fields

Required

targets (type=list of RepresentativeMicrohaplotypesForTarget)
- a list of the microhaplotype for each targets

Example

Code

RepresentativeMicrohaplotypesForTarget

https://plasmogenepi.github.io/portable-microhaplotype-object/RepresentativeMicrohaplotypesForTarget/
Show RepresentativeMicrohaplotypesForTarget fields

Required

target_id (type=integer)
- the index into the target_info list
microhaplotypes (type=list of RepresentativeMicrohaplotype)
- a list of the microhaplotypes detected for a target

Optional

mhap_location (type=GenomicLocation)
- a genomic location that was analyzed for this target info, this allows listing location that may be different from the full target location (e.g 1 base in from the full)

Example

Code

SequencingInfo

https://plasmogenepi.github.io/portable-microhaplotype-object/SequencingInfo/
Show SequencingInfo fields

Required

sequencing_info_name (type=string)
- a name of for the sequencing done, e.g. batch1
seq_platform (type=string)
- the sequencing technology used to sequence the run, e.g. ILLUMINA, NANOPORE, PACBIO
seq_instrument_model (type=string)
- the sequencing instrument model used to sequence the run, e.g. NextSeq 2000, MinION, Revio
library_layout (type=string)
- Specify the configuration of reads, e.g. paired-end, single
library_strategy (type=string)
- what the nuceloacid sequencing/amplification strategy was (common names are AMPLICON, WGS)
library_source (type=string)
- Source of amplification material (common names GENOMIC, TRANSCRIPTOMIC)
library_selection (type=string)
- how amplification was done (common are PCR=Source material was selected by designed primers, RANDOM =Random selection by shearing or other method)

Optional

library_kit (type=string)
- Name, version, and applicable cell or cycle numbers for the kit used to prepare libraries and load cells or chips for sequencing. If possible, include a part number, e.g. MiSeq Reagent Kit v3 (150-cycle), MS-102-3001
library_screen (type=string)
- Describe enrichment, screening, or normalization methods applied during amplification or library preparation, e.g. size selection 390bp, diluted to 1 ng DNA/sample
nucl_acid_amp (type=string)
- Link to a reference or kit that describes the enzymatic amplification of nucleic acids
nucl_acid_amp_date (type=string)
- the date of the nucleoacid amplification
nucl_acid_ext (type=string)
- Link to a reference or kit that describes the recovery of nucleic acids from the sample
nucl_acid_ext_date (type=string)
- the date of the nucleoacid extraction
pcr_cond (type=string)
- the method/conditions for PCR, List PCR cycles used to amplify the target
seq_center (type=string)
- Name of facility where sequencing was performed (lab, core facility, or company)
seq_date (type=string)
- the date of sequencing, should be YYYY-MM or YYYY-MM-DD

Example

Code

SpecimenInfo

https://plasmogenepi.github.io/portable-microhaplotype-object/SpecimenInfo/
Show SpecimenInfo fields

Required

specimen_name (type=string)
- an identifier for the specimen, should be unique within this sample set
specimen_taxon_id (type= list of integer)
- the NCBI taxonomy number of the organism in specimen, can list multiple if a mixed sample
host_taxon_id (type=integer)
- the NCBI taxonomy number of the host that the specimen was collected from
collection_date (type=string)
- the date of the specimen collection, can be YYYY, YYYY-MM, or YYYY-MM-DD
collection_country (type=string)
- the name of country collected in, would be the same as admin level 0
project_id (type=integer)
- the index into the project_info list

Optional

alternate_identifiers (type=list of string)
- a list of optional alternative names
blood_meal (type=boolean)
- whether host specimen has had a recent blood meal
drug_usage (type=list of string)
- Any drug used by subject and the frequency of usage; can include multiple drugs used
env_broad_scale (type=string)
- the broad environment from which the specimen was collected, e.g. highlands, lowlands, mountainous region
env_local_scale (type=string)
- the local environment from which the specimen was collected, e.g. jungle, urban, rural
env_medium (type=string)
- the environment medium from which the specimen was collected from
geo_admin1 (type=string)
- geographical admin level 1, the secondary large demarcation of a nation (nation = admin level 0)
geo_admin2 (type=string)
- geographical admin level 2, the third large demarcation of a nation (nation = admin level 0)
geo_admin3 (type=string)
- geographical admin level 3, the third large demarcation of a nation (nation = admin level 0)
gravid (type=boolean)
- whether host specimen is currently pregnant
gravidity (type=integer)
- the gravidity of the specimen host (number of previous pregnancies)
has_travel_out_six_month (type=boolean)
- has travelled out from local region in the last six months
host_age (type=number)
- if specimen is from a person, the age in years of the person, can be float value so for 3 month old put 0.25
host_sex (type=string)
- if specimen is from a person, the sex listed for that person
host_subject_id (type=integer)
- an identifier for the individual a specimen was collected from
lat_lon (type=string)
- the latitude and longitude of a specific site
parasite_density_info (type=list of ParasiteDensity)
- one or more parasite densities in microliters for this specimen
specimen_accession (type=string)
- if specimen is deposited in a database, what accession is it associated with
specimen_collect_device (type=string)
- the way the specimen was collected, e.g. whole blood, dried blood spot
specimen_comments (type=list of string)
- any additional comments about the specimen
specimen_store_loc (type=string)
- the specimen store site, address or facility name
specimen_type (type=string)
- what type of specimen this is, e.g. negative_control, positive_control, field_sample
storage_plate_info (type=PlateInfo)
- plate location of where specimen is stored if stored in a plate
travel_out_six_month (type=list of TravelInfo)
- Specification of the countries travelled in the last six months; can include multiple travels
treatment_status (type=list of string)
- If person has been treated with drugs, what was the treatment outcome

Example

Code

StageReadCounts

https://plasmogenepi.github.io/portable-microhaplotype-object/StageReadCounts/
Show StageReadCounts fields

Required

read_count (type=integer)
- the read counts
stage (type=string)
- the stage of the pipeline, e.g. demultiplexed, denoised, etc

Example

Code

TargetInfo

https://plasmogenepi.github.io/portable-microhaplotype-object/TargetInfo/
Show TargetInfo fields

Required

target_name (type=string)
- an identifier for this target
forward_primer (type=PrimerInfo)
- the forward primer associated with this target
reverse_primer (type=PrimerInfo)
- the reverse primer associated with this target

Optional

gene_name (type=string)
- an identifier of the gene, if any, is being covered with this targeted
insert_location (type=GenomicLocation)
- the intended genomic location of the insert of the amplicon (the location between the end of the forward primer and the beginning of the reverse primer)
markers_of_interest (type=list of MarkerOfInterest)
- a list of covered markers of interest
target_attributes (type=list of string)
- a list of classification type for the primer target

Example

Code

TravelInfo

https://plasmogenepi.github.io/portable-microhaplotype-object/TravelInfo/
Show TravelInfo fields

Required

travel_country (type=string)
- the name of country, would be the same as admin level 0
travel_start_date (type=string)
- the date of the start of travel, can be approximate, should be YYYY-MM or YYYY-MM-DD (preferred)
travel_end_date (type=string)
- the date of the end of travel, can be approximate, should be YYYY-MM or YYYY-MM-DD (preferred)

Optional

bed_net_usage (type=number)
- approximate usage of bed net while traveling, 1 = 100% nights with bed net, 0 = 0% no bed net usage
geo_admin1 (type=string)
- geographical admin level 1, the secondary large demarcation of a nation (nation = admin level 0)
geo_admin2 (type=string)
- geographical admin level 2, the third large demarcation of a nation (nation = admin level 0)
geo_admin3 (type=string)
- geographical admin level 3, the third large demarcation of a nation (nation = admin level 0)
lat_lon (type=string)
- the latitude and longitude of a specific site

Example

Code

--- title: "Format Overview For Developers" --- ```{r setup, echo=FALSE} source("../common.R") ``` # Python implementation Linkml generates a datamodel file with all classes: <https://github.com/PlasmoGenEpi/portable-micorhaplotype-object/blob/main/src/plasmo_tar_amp_schema/datamodel/plasmo_tar_amp_schema.py> # Tools Started development of a tool called pmotools. Python implementation can be found here: <https://github.com/PlasmoGenEpi/pmotools-python/tree/develop> # Format overview Below is an overview of the entire format currently in development which is under active development and optimization. Please send questions to [info@plasmogenepi.org](mailto:info@plasmogenepi.org) :::{.column-screen} ```{r, echo=FALSE, results="asis"} cat(readr::read_lines("portable_microhaplotype_object.schema.dot.svg", skip = 6), sep = "\n") ``` ::: ## PortableMicrohaplotypeObject <https://plasmogenepi.github.io/portable-microhaplotype-object/PortableMicrohaplotypeObject/> ### Required * library_sample_info (***type=[list of LibrarySampleInfo](#librarysampleinfo)***) * a list of libraries of all the seq/amp of the specimens within this project * specimen_info (***type=[list of SpecimenInfo](#specimeninfo)***) * a list of all the specimens within this project * sequencing_info (***type=[list of SequencingInfo](#sequencinginfo)***) * a list of sequencing info for this project * panel_info (***type=[list of PanelInfo](#panelinfo)***) * a list of info on the panels * target_info (***type=[list of TargetInfo](#targetinfo)***) * a list of info on the targets * targeted_genomes (***type=[list of GenomeInfo](#genomeinfo)***) * a list of genomes that the targets in TargetInfo refer to * representative_microhaplotypes (***type=[RepresentativeMicrohaplotypes](#representativemicrohaplotypes)***) * a list of the information on the representative microhaplotypes * bioinformatics_methods_info (***type=[list of BioinformaticsMethodInfo](#bioinformaticsmethodinfo)***) * the bioinformatics pipeline/methods used to generated the amplicon analysis for this project * bioinformatics_run_info (***type=[list of BioinformaticsRunInfo](#bioinformaticsruninfo)***) * the runtime info for the bioinformatics pipeline used to generated the amplicon analysis for this project * detected_microhaplotypes (***type=[list of DetectedMicrohaplotypes](#detectedmicrohaplotypes)***) * the microhaplotypes detected in this projects * project_info (***type=[list of ProjectInfo](#projectinfo)***) * the information about the projects stored in this PMO * pmo_header (***type=[PmoHeader](#pmoheader)***) * the PMO information for this file including version etc ### Optional * read_counts_by_stage (***type=[list of ReadCountsByStage](#readcountsbystage)***) * the read counts for different stages of the pipeline ### Example ```{json} ``` ## BioMethod <https://plasmogenepi.github.io/portable-microhaplotype-object/BioMethod/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseBioMethod" aria-expanded="false" aria-controls="collapseExample"> Show BioMethod fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseBioMethod"> <div class="card card-body"> ### Required * program_version (***type=string***) * the version of generation method, should be in the format of v[MAJOR].[MINOR].[PATCH] * program (***type=string***) * name of the program used for this portion of the pipeline ### Optional * additional_argument (***type=list of string***) * any additional arguments that differ from the default * program_description (***type=string***) * a short description of what this method does * program_url (***type=string***) * a url pointing to code base of a program, e.g. a github link ### Example ```{json} ``` </div> </div><br> ## BioinformaticsMethodInfo <https://plasmogenepi.github.io/portable-microhaplotype-object/BioinformaticsMethodInfo/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseBioinformaticsMethodInfo" aria-expanded="false" aria-controls="collapseExample"> Show BioinformaticsMethodInfo fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseBioinformaticsMethodInfo"> <div class="card card-body"> ### Required * demultiplexing_method (***type=[BioMethod](#biomethod)***) * the demultiplexing method used to separate raw reads from barcodes and primer targets * denoising_method (***type=[BioMethod](#biomethod)***) * the method used to de-noise and/or cluster the raw reads ### Optional * additional_methods (***type=[list of BioMethod](#biomethod)***) * any additional methods used to analyze the data * bioinformatics_method_name (***type=string***) * name of the collection of methods is called, e.g. pipeline ### Example ```{json} ``` </div> </div><br> ## BioinformaticsRunInfo <https://plasmogenepi.github.io/portable-microhaplotype-object/BioinformaticsRunInfo/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseBioinformaticsRunInfo" aria-expanded="false" aria-controls="collapseExample"> Show BioinformaticsRunInfo fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseBioinformaticsRunInfo"> <div class="card card-body"> ### Required * bioinformatics_methods_id (***type=integer***) * the index into the bioinformatics_methods_info list * bioinformatics_run_name (***type=string***) * a name to for this run, needs to be unique to each run ### Optional * run_date (***type=string***) * the date when the run was done, should be YYYY-MM-DD ### Example ```{json} ``` </div> </div><br> ## DetectedMicrohaplotypes <https://plasmogenepi.github.io/portable-microhaplotype-object/DetectedMicrohaplotypes/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseDetectedMicrohaplotypes" aria-expanded="false" aria-controls="collapseExample"> Show DetectedMicrohaplotypes fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseDetectedMicrohaplotypes"> <div class="card card-body"> ### Required * bioinformatics_run_id (***type=integer***) * the index into bioinformatics_run_info list * library_samples (***type=[list of DetectedMicrohaplotypesForSample](#detectedmicrohaplotypesforsample)***) * a list of the microhaplotypes detected for a sample by targets ### Example ```{json} ``` </div> </div><br> ## DetectedMicrohaplotypesForSample <https://plasmogenepi.github.io/portable-microhaplotype-object/DetectedMicrohaplotypesForSample/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseDetectedMicrohaplotypesForSample" aria-expanded="false" aria-controls="collapseExample"> Show DetectedMicrohaplotypesForSample fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseDetectedMicrohaplotypesForSample"> <div class="card card-body"> ### Required * library_sample_id (***type=integer***) * the index into the library_sample_info list * target_results (***type=[list of DetectedMicrohaplotypesForTarget](#detectedmicrohaplotypesfortarget)***) * a list of the microhaplotypes detected for a list of targets ### Example ```{json} ``` </div> </div><br> ## DetectedMicrohaplotypesForTarget <https://plasmogenepi.github.io/portable-microhaplotype-object/DetectedMicrohaplotypesForTarget/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseDetectedMicrohaplotypesForTarget" aria-expanded="false" aria-controls="collapseExample"> Show DetectedMicrohaplotypesForTarget fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseDetectedMicrohaplotypesForTarget"> <div class="card card-body"> ### Required * mhaps_target_id (***type=integer***) * the index for a target in the representative_microhaplotypes list * mhaps (***type=[list of MicrohaplotypeForTarget](#microhaplotypefortarget)***) * a list of the microhaplotypes detected for this target ### Example ```{json} ``` </div> </div><br> ## GenomeInfo <https://plasmogenepi.github.io/portable-microhaplotype-object/GenomeInfo/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseGenomeInfo" aria-expanded="false" aria-controls="collapseExample"> Show GenomeInfo fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseGenomeInfo"> <div class="card card-body"> ### Required * name (***type=string***) * name of the genome * genome_version (***type=string***) * the genome version * taxon_id (***type= list of integer***) * the NCBI taxonomy number, can be a list of values * url (***type=string***) * a link to the where this genome file could be downloaded ### Optional * chromosomes (***type=list of string***) * a list of chromosomes found within this genome * gff_url (***type=string***) * a link to the where this genome's annotation file could be downloaded ### Example ```{json} ``` </div> </div><br> ## GenomicLocation <https://plasmogenepi.github.io/portable-microhaplotype-object/GenomicLocation/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseGenomicLocation" aria-expanded="false" aria-controls="collapseExample"> Show GenomicLocation fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseGenomicLocation"> <div class="card card-body"> ### Required * genome_id (***type=integer***) * the index to the genome in the targeted_genomes list that this location refers to * chrom (***type=string***) * the chromosome name * start (***type=integer***) * the start of the location, 0-based positioning * end (***type=integer***) * the end of the location, 0-based positioning ### Optional * alt_seq (***type=string***) * a possible alternative sequence of this genomic location * ref_seq (***type=string***) * the reference sequence of this genomic location * strand (***type=string***) * which strand the location is, either + for plus strand or - for negative strand ### Example ```{json} ``` </div> </div><br> ## LibrarySampleInfo <https://plasmogenepi.github.io/portable-microhaplotype-object/LibrarySampleInfo/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseLibrarySampleInfo" aria-expanded="false" aria-controls="collapseExample"> Show LibrarySampleInfo fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseLibrarySampleInfo"> <div class="card card-body"> ### Required * sequencing_info_id (***type=integer***) * the index into the sequencing_info list * specimen_id (***type=integer***) * the index into the specimen_info list * panel_id (***type=integer***) * the index into the panel_info list * library_sample_name (***type=string***) * a unique identifier for this sequence/amplification run on a specimen_name ### Optional * alternate_identifiers (***type=list of string***) * a list of optional alternative names * experiment_accession (***type=string***) * ERA/SRA experiment accession number for the sample if it was submitted * fastqs_loc (***type=string***) * the location (url or filename path) of the fastqs for a library run * library_prep_plate_info (***type=[PlateInfo](#plateinfo)***) * plate location of where library was prepared for sequencing * qpcr_parasite_density_info (***type=[list of ParasiteDensity](#parasitedensity)***) * qpcr parasite density measurement for this extracted sample * run_accession (***type=string***) * ERA/SRA run accession number for the sample if it was submitted ### Example ```{json} ``` </div> </div><br> ## MarkerOfInterest <https://plasmogenepi.github.io/portable-microhaplotype-object/MarkerOfInterest/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseMarkerOfInterest" aria-expanded="false" aria-controls="collapseExample"> Show MarkerOfInterest fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseMarkerOfInterest"> <div class="card card-body"> ### Required * marker_location (***type=[GenomicLocation](#genomiclocation)***) * the genomic location ### Optional * associations (***type=list of string***) * a list of associations with this marker, e.g. SP resistance, etc ### Example ```{json} ``` </div> </div><br> ## MaskingInfo <https://plasmogenepi.github.io/portable-microhaplotype-object/MaskingInfo/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseMaskingInfo" aria-expanded="false" aria-controls="collapseExample"> Show MaskingInfo fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseMaskingInfo"> <div class="card card-body"> ### Required * seq_start (***type=integer***) * the start of the masking * seq_segment_size (***type=integer***) * the size of the masking * replacement_size (***type=integer***) * the size of replacement mask ### Optional * masking_generation_description (***type=string***) * a description of how the masking information was generated ### Example ```{json} ``` </div> </div><br> ## MicrohaplotypeForTarget <https://plasmogenepi.github.io/portable-microhaplotype-object/MicrohaplotypeForTarget/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseMicrohaplotypeForTarget" aria-expanded="false" aria-controls="collapseExample"> Show MicrohaplotypeForTarget fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseMicrohaplotypeForTarget"> <div class="card card-body"> ### Required * mhap_id (***type=integer***) * the index for a microhaplotype for a target in the representative_microhaplotypes list, e.g. representative_microhaplotypes[mhaps_target_id][mhap_id] * reads (***type=integer***) * the read count associated with this microhaplotype ### Optional * umis (***type=integer***) * the unique molecular identifier (umi) count associated with this microhaplotype ### Example ```{json} ``` </div> </div><br> ## PanelInfo <https://plasmogenepi.github.io/portable-microhaplotype-object/PanelInfo/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapsePanelInfo" aria-expanded="false" aria-controls="collapseExample"> Show PanelInfo fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapsePanelInfo"> <div class="card card-body"> ### Required * reactions (***type=[list of ReactionInfo](#reactioninfo)***) * a list of 1 or more reactions that this panel contains, each reactions list the targets that were amplified in that reaction, e.g. pool1, pool2 * panel_name (***type=string***) * a name for the panel ### Example ```{json} ``` </div> </div><br> ## ParasiteDensity <https://plasmogenepi.github.io/portable-microhaplotype-object/ParasiteDensity/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseParasiteDensity" aria-expanded="false" aria-controls="collapseExample"> Show ParasiteDensity fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseParasiteDensity"> <div class="card card-body"> ### Required * parasite_density_method (***type=string***) * the method of how this density was obtained * parasite_density (***type=number***) * the density in microliters ### Optional * date_measured (***type=string***) * the date the qpcr was performed, can be YYYY, YYYY-MM, or YYYY-MM-DD * density_method_comments (***type=string***) * additional comments about how the density was performed ### Example ```{json} ``` </div> </div><br> ## PlateInfo <https://plasmogenepi.github.io/portable-microhaplotype-object/PlateInfo/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapsePlateInfo" aria-expanded="false" aria-controls="collapseExample"> Show PlateInfo fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapsePlateInfo"> <div class="card card-body"> ### Required ### Optional * plate_col (***type=integer***) * the column the specimen was in * plate_name (***type=string***) * a name of plate the specimen was in * plate_row (***type=string***) * the row the specimen was in ### Example ```{json} ``` </div> </div><br> ## PmoGenerationMethod <https://plasmogenepi.github.io/portable-microhaplotype-object/PmoGenerationMethod/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapsePmoGenerationMethod" aria-expanded="false" aria-controls="collapseExample"> Show PmoGenerationMethod fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapsePmoGenerationMethod"> <div class="card card-body"> ### Required * program_version (***type=string***) * the version of generation method, should be in the format of v[MAJOR].[MINOR].[PATCH] * program_name (***type=string***) * the name of the program ### Example ```{json} ``` </div> </div><br> ## PmoHeader <https://plasmogenepi.github.io/portable-microhaplotype-object/PmoHeader/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapsePmoHeader" aria-expanded="false" aria-controls="collapseExample"> Show PmoHeader fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapsePmoHeader"> <div class="card card-body"> ### Required * pmo_version (***type=string***) * the version of the PMO file, should be in the format of v[MAJOR].[MINOR].[PATCH] ### Optional * creation_date (***type=string***) * the date of when the PMO file was created or modified, should be YYYY-MM-DD * generation_method (***type=[PmoGenerationMethod](#pmogenerationmethod)***) * the generation method to create this PMO ### Example ```{json} ``` </div> </div><br> ## PrimerInfo <https://plasmogenepi.github.io/portable-microhaplotype-object/PrimerInfo/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapsePrimerInfo" aria-expanded="false" aria-controls="collapseExample"> Show PrimerInfo fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapsePrimerInfo"> <div class="card card-body"> ### Required * seq (***type=string***) * the DNA sequence ### Optional * location (***type=[GenomicLocation](#genomiclocation)***) * what the intended genomic location of the primer is ### Example ```{json} ``` </div> </div><br> ## ProjectInfo <https://plasmogenepi.github.io/portable-microhaplotype-object/ProjectInfo/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseProjectInfo" aria-expanded="false" aria-controls="collapseExample"> Show ProjectInfo fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseProjectInfo"> <div class="card card-body"> ### Required * project_name (***type=string***) * a name for the project, should be unique if multiple projects listed * project_description (***type=string***) * a short description of the project ### Optional * BioProject_accession (***type=string***) * an SRA bioproject accession e.g. PRJNA33823 * project_collector_chief_scientist (***type=string***) * can be collection of names separated by a semicolon if multiple people involved or can just be the name of the primary person managing the specimen * project_contributors (***type=list of string***) * a list of collaborators who contributed to this project * project_type (***type=string***) * the type of project conducted, e.g. TES vs surveillance vs transmission ### Example ```{json} ``` </div> </div><br> ## ProteinVariant <https://plasmogenepi.github.io/portable-microhaplotype-object/ProteinVariant/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseProteinVariant" aria-expanded="false" aria-controls="collapseExample"> Show ProteinVariant fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseProteinVariant"> <div class="card card-body"> ### Required * protein_location (***type=[GenomicLocation](#genomiclocation)***) * the position within the protein, the chromosome in this case would be the transcript name ### Optional * alternative_gene_name (***type=string***) * an alternative gene name * codon_genomic_location (***type=[GenomicLocation](#genomiclocation)***) * the position within the genomic sequence of the codon * gene_name (***type=string***) * an identifier of the gene, if any, is being covered with this targeted ### Example ```{json} ``` </div> </div><br> ## Pseudocigar <https://plasmogenepi.github.io/portable-microhaplotype-object/Pseudocigar/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapsePseudocigar" aria-expanded="false" aria-controls="collapseExample"> Show Pseudocigar fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapsePseudocigar"> <div class="card card-body"> ### Required * pseudocigar_seq (***type=string***) * the pseudocigar itself * ref_loc (***type=[GenomicLocation](#genomiclocation)***) * the genomic location the pseudocigar is in reference to ### Optional * pseudocigar_generation_description (***type=string***) * a description of how the pseudocigar information was generated ### Example ```{json} ``` </div> </div><br> ## ReactionInfo <https://plasmogenepi.github.io/portable-microhaplotype-object/ReactionInfo/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseReactionInfo" aria-expanded="false" aria-controls="collapseExample"> Show ReactionInfo fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseReactionInfo"> <div class="card card-body"> ### Required * panel_targets (***type= list of integer***) * a list of the target indexes in the target_info list * reaction_name (***type=string***) * a name for this reaction ### Example ```{json} ``` </div> </div><br> ## ReadCountsByStage <https://plasmogenepi.github.io/portable-microhaplotype-object/ReadCountsByStage/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseReadCountsByStage" aria-expanded="false" aria-controls="collapseExample"> Show ReadCountsByStage fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseReadCountsByStage"> <div class="card card-body"> ### Required * bioinformatics_run_id (***type=integer***) * the index into bioinformatics_run_info list * read_counts_by_library_sample_by_stage (***type=[list of ReadCountsByStageForLibrarySample](#readcountsbystageforlibrarysample)***) * a list by library_sample for the counts at each stage ### Example ```{json} ``` </div> </div><br> ## ReadCountsByStageForLibrarySample <https://plasmogenepi.github.io/portable-microhaplotype-object/ReadCountsByStageForLibrarySample/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseReadCountsByStageForLibrarySample" aria-expanded="false" aria-controls="collapseExample"> Show ReadCountsByStageForLibrarySample fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseReadCountsByStageForLibrarySample"> <div class="card card-body"> ### Required * library_sample_id (***type=integer***) * the index into the library_sample_info list * total_raw_count (***type=integer***) * the raw counts off the sequencing machine that a sample began with ### Optional * read_counts_for_targets (***type=[list of ReadCountsByStageForTarget](#readcountsbystagefortarget)***) * a list of counts by stage for a target ### Example ```{json} ``` </div> </div><br> ## ReadCountsByStageForTarget <https://plasmogenepi.github.io/portable-microhaplotype-object/ReadCountsByStageForTarget/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseReadCountsByStageForTarget" aria-expanded="false" aria-controls="collapseExample"> Show ReadCountsByStageForTarget fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseReadCountsByStageForTarget"> <div class="card card-body"> ### Required * target_id (***type=integer***) * the index into the target_info list * stages (***type=[list of StageReadCounts](#stagereadcounts)***) * the read counts by each stage ### Example ```{json} ``` </div> </div><br> ## RepresentativeMicrohaplotype <https://plasmogenepi.github.io/portable-microhaplotype-object/RepresentativeMicrohaplotype/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseRepresentativeMicrohaplotype" aria-expanded="false" aria-controls="collapseExample"> Show RepresentativeMicrohaplotype fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseRepresentativeMicrohaplotype"> <div class="card card-body"> ### Required * seq (***type=string***) * the DNA sequence ### Optional * alt_annotations (***type=list of string***) * a list of additional annotations associated with this microhaplotype, e.g. wildtype * associated_protein_variants (***type=[list of ProteinVariant](#proteinvariant)***) * a list of associated protein variants with this haplotype, e.g. amino acid changes/INDELS * associated_seq_variants (***type=[list of GenomicLocation](#genomiclocation)***) * a list of associated sequence variants with this haplotype, e.g. SNPS, indels * masking (***type=[list of MaskingInfo](#maskinginfo)***) * masking info for the sequence * microhaplotype_name (***type=string***) * an optional name for this microhaplotype * pseudocigar (***type=[Pseudocigar](#pseudocigar)***) * the pseudocigar of the haplotype * quality (***type=string***) * the ansi fastq per base quality score for this sequence, this is optional ### Example ```{json} ``` </div> </div><br> ## RepresentativeMicrohaplotypes <https://plasmogenepi.github.io/portable-microhaplotype-object/RepresentativeMicrohaplotypes/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseRepresentativeMicrohaplotypes" aria-expanded="false" aria-controls="collapseExample"> Show RepresentativeMicrohaplotypes fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseRepresentativeMicrohaplotypes"> <div class="card card-body"> ### Required * targets (***type=[list of RepresentativeMicrohaplotypesForTarget](#representativemicrohaplotypesfortarget)***) * a list of the microhaplotype for each targets ### Example ```{json} ``` </div> </div><br> ## RepresentativeMicrohaplotypesForTarget <https://plasmogenepi.github.io/portable-microhaplotype-object/RepresentativeMicrohaplotypesForTarget/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseRepresentativeMicrohaplotypesForTarget" aria-expanded="false" aria-controls="collapseExample"> Show RepresentativeMicrohaplotypesForTarget fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseRepresentativeMicrohaplotypesForTarget"> <div class="card card-body"> ### Required * target_id (***type=integer***) * the index into the target_info list * microhaplotypes (***type=[list of RepresentativeMicrohaplotype](#representativemicrohaplotype)***) * a list of the microhaplotypes detected for a target ### Optional * mhap_location (***type=[GenomicLocation](#genomiclocation)***) * a genomic location that was analyzed for this target info, this allows listing location that may be different from the full target location (e.g 1 base in from the full) ### Example ```{json} ``` </div> </div><br> ## SequencingInfo <https://plasmogenepi.github.io/portable-microhaplotype-object/SequencingInfo/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseSequencingInfo" aria-expanded="false" aria-controls="collapseExample"> Show SequencingInfo fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseSequencingInfo"> <div class="card card-body"> ### Required * sequencing_info_name (***type=string***) * a name of for the sequencing done, e.g. batch1 * seq_platform (***type=string***) * the sequencing technology used to sequence the run, e.g. ILLUMINA, NANOPORE, PACBIO * seq_instrument_model (***type=string***) * the sequencing instrument model used to sequence the run, e.g. NextSeq 2000, MinION, Revio * library_layout (***type=string***) * Specify the configuration of reads, e.g. paired-end, single * library_strategy (***type=string***) * what the nuceloacid sequencing/amplification strategy was (common names are AMPLICON, WGS) * library_source (***type=string***) * Source of amplification material (common names GENOMIC, TRANSCRIPTOMIC) * library_selection (***type=string***) * how amplification was done (common are PCR=Source material was selected by designed primers, RANDOM =Random selection by shearing or other method) ### Optional * library_kit (***type=string***) * Name, version, and applicable cell or cycle numbers for the kit used to prepare libraries and load cells or chips for sequencing. If possible, include a part number, e.g. MiSeq Reagent Kit v3 (150-cycle), MS-102-3001 * library_screen (***type=string***) * Describe enrichment, screening, or normalization methods applied during amplification or library preparation, e.g. size selection 390bp, diluted to 1 ng DNA/sample * nucl_acid_amp (***type=string***) * Link to a reference or kit that describes the enzymatic amplification of nucleic acids * nucl_acid_amp_date (***type=string***) * the date of the nucleoacid amplification * nucl_acid_ext (***type=string***) * Link to a reference or kit that describes the recovery of nucleic acids from the sample * nucl_acid_ext_date (***type=string***) * the date of the nucleoacid extraction * pcr_cond (***type=string***) * the method/conditions for PCR, List PCR cycles used to amplify the target * seq_center (***type=string***) * Name of facility where sequencing was performed (lab, core facility, or company) * seq_date (***type=string***) * the date of sequencing, should be YYYY-MM or YYYY-MM-DD ### Example ```{json} ``` </div> </div><br> ## SpecimenInfo <https://plasmogenepi.github.io/portable-microhaplotype-object/SpecimenInfo/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseSpecimenInfo" aria-expanded="false" aria-controls="collapseExample"> Show SpecimenInfo fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseSpecimenInfo"> <div class="card card-body"> ### Required * specimen_name (***type=string***) * an identifier for the specimen, should be unique within this sample set * specimen_taxon_id (***type= list of integer***) * the NCBI taxonomy number of the organism in specimen, can list multiple if a mixed sample * host_taxon_id (***type=integer***) * the NCBI taxonomy number of the host that the specimen was collected from * collection_date (***type=string***) * the date of the specimen collection, can be YYYY, YYYY-MM, or YYYY-MM-DD * collection_country (***type=string***) * the name of country collected in, would be the same as admin level 0 * project_id (***type=integer***) * the index into the project_info list ### Optional * alternate_identifiers (***type=list of string***) * a list of optional alternative names * blood_meal (***type=boolean***) * whether host specimen has had a recent blood meal * drug_usage (***type=list of string***) * Any drug used by subject and the frequency of usage; can include multiple drugs used * env_broad_scale (***type=string***) * the broad environment from which the specimen was collected, e.g. highlands, lowlands, mountainous region * env_local_scale (***type=string***) * the local environment from which the specimen was collected, e.g. jungle, urban, rural * env_medium (***type=string***) * the environment medium from which the specimen was collected from * geo_admin1 (***type=string***) * geographical admin level 1, the secondary large demarcation of a nation (nation = admin level 0) * geo_admin2 (***type=string***) * geographical admin level 2, the third large demarcation of a nation (nation = admin level 0) * geo_admin3 (***type=string***) * geographical admin level 3, the third large demarcation of a nation (nation = admin level 0) * gravid (***type=boolean***) * whether host specimen is currently pregnant * gravidity (***type=integer***) * the gravidity of the specimen host (number of previous pregnancies) * has_travel_out_six_month (***type=boolean***) * has travelled out from local region in the last six months * host_age (***type=number***) * if specimen is from a person, the age in years of the person, can be float value so for 3 month old put 0.25 * host_sex (***type=string***) * if specimen is from a person, the sex listed for that person * host_subject_id (***type=integer***) * an identifier for the individual a specimen was collected from * lat_lon (***type=string***) * the latitude and longitude of a specific site * parasite_density_info (***type=[list of ParasiteDensity](#parasitedensity)***) * one or more parasite densities in microliters for this specimen * specimen_accession (***type=string***) * if specimen is deposited in a database, what accession is it associated with * specimen_collect_device (***type=string***) * the way the specimen was collected, e.g. whole blood, dried blood spot * specimen_comments (***type=list of string***) * any additional comments about the specimen * specimen_store_loc (***type=string***) * the specimen store site, address or facility name * specimen_type (***type=string***) * what type of specimen this is, e.g. negative_control, positive_control, field_sample * storage_plate_info (***type=[PlateInfo](#plateinfo)***) * plate location of where specimen is stored if stored in a plate * travel_out_six_month (***type=[list of TravelInfo](#travelinfo)***) * Specification of the countries travelled in the last six months; can include multiple travels * treatment_status (***type=list of string***) * If person has been treated with drugs, what was the treatment outcome ### Example ```{json} ``` </div> </div><br> ## StageReadCounts <https://plasmogenepi.github.io/portable-microhaplotype-object/StageReadCounts/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseStageReadCounts" aria-expanded="false" aria-controls="collapseExample"> Show StageReadCounts fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseStageReadCounts"> <div class="card card-body"> ### Required * read_count (***type=integer***) * the read counts * stage (***type=string***) * the stage of the pipeline, e.g. demultiplexed, denoised, etc ### Example ```{json} ``` </div> </div><br> ## TargetInfo <https://plasmogenepi.github.io/portable-microhaplotype-object/TargetInfo/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseTargetInfo" aria-expanded="false" aria-controls="collapseExample"> Show TargetInfo fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseTargetInfo"> <div class="card card-body"> ### Required * target_name (***type=string***) * an identifier for this target * forward_primer (***type=[PrimerInfo](#primerinfo)***) * the forward primer associated with this target * reverse_primer (***type=[PrimerInfo](#primerinfo)***) * the reverse primer associated with this target ### Optional * gene_name (***type=string***) * an identifier of the gene, if any, is being covered with this targeted * insert_location (***type=[GenomicLocation](#genomiclocation)***) * the intended genomic location of the insert of the amplicon (the location between the end of the forward primer and the beginning of the reverse primer) * markers_of_interest (***type=[list of MarkerOfInterest](#markerofinterest)***) * a list of covered markers of interest * target_attributes (***type=list of string***) * a list of classification type for the primer target ### Example ```{json} ``` </div> </div><br> ## TravelInfo <https://plasmogenepi.github.io/portable-microhaplotype-object/TravelInfo/> <a class = "btn btn-light" data-bs-toggle="collapse" data-bs-target="#collapseTravelInfo" aria-expanded="false" aria-controls="collapseExample"> Show TravelInfo fields <i class="fa-solid fa-caret-right"></i> </a> <div class="collapse" id="collapseTravelInfo"> <div class="card card-body"> ### Required * travel_country (***type=string***) * the name of country, would be the same as admin level 0 * travel_start_date (***type=string***) * the date of the start of travel, can be approximate, should be YYYY-MM or YYYY-MM-DD (preferred) * travel_end_date (***type=string***) * the date of the end of travel, can be approximate, should be YYYY-MM or YYYY-MM-DD (preferred) ### Optional * bed_net_usage (***type=number***) * approximate usage of bed net while traveling, 1 = 100% nights with bed net, 0 = 0% no bed net usage * geo_admin1 (***type=string***) * geographical admin level 1, the secondary large demarcation of a nation (nation = admin level 0) * geo_admin2 (***type=string***) * geographical admin level 2, the third large demarcation of a nation (nation = admin level 0) * geo_admin3 (***type=string***) * geographical admin level 3, the third large demarcation of a nation (nation = admin level 0) * lat_lon (***type=string***) * the latitude and longitude of a specific site ### Example ```{json} ``` </div> </div><br> {{< fa dna >}}