PMO Examples

Minimum PMO example

S_aureus

Contains the PMO for the S. aureus dataset - Furstenau2025_PMO.json.gz. This PMO was contructed from SRA-sourced data(Furstenau et al. 2025)

minimum_Furstenau2025_PMO.json.gz

Example data from PMO manuscript

ANOSPP

Anopheles and Plasmodium data obtained from 4128 mosquito samples from Gabon that were sequenced as part of the ANOSPP (ANOpheles SPecies identification and Plasmodium detection) project(Makunin et al. 2021)

anospp_pmo.json.gz

GENE8

Public genomic surveillance data of Plasmodium falciparum from four countries: Eswatini, Namibia, South Africa, and Zambia. This folder contains input files, intermediate PMOs, and processing notebooks [Aranda-Díaz et al. (2025)](Eloff et al. 2025)[Nhlengethwa et al. (2025)](Raman et al. 2025)

dataset1_pmo_qc_pass.json.gz

mips_v_mad4hatter

Contains the PMO containing specimens that were sequenced using both the MAD4HatTeR amplicon sequencing and the DR23K molecular inversion probe (MIP) assay (Katairo et al. 2025)

PRJNA1252738_PMO.json.gz

E_coli

Contains the PMO for the E. coli dataset - e_coli_coliseq_PMO.json.gz. This PMO was contructed from SRA-sourced data(Williamson et al. 2024)

e_coli_coliseq_PMO.json.gz

S_aureus

Contains the PMO for the S. aureus dataset - Furstenau2025_PMO.json.gz. This PMO was contructed from SRA-sourced data(Furstenau et al. 2025)

Furstenau2025_PMO.json.gz

Additional Example data format

Example created from a study from Mozambique(Tessema et al. 2022)

https://academic.oup.com/jid/article/225/7/1227/5897005

moz2018_PMO.json.gz

From Pf7+ data for the same panel above

Global data microhaplotypes were constructed by PathWeaver for the same targeted amplicon panel above. This includes approximately 1900 samples.

PathWeaverHeome1_PMO.json.gz

References

Aranda-Díaz, Andrés, Sydney Mwanza, Takalani I Makhanthisa, et al. 2025. “Plasmodium Falciparum Genomic Surveillance Reveals a Diversity of Kelch 13 Mutations in Zambia.” Am. J. Trop. Med. Hyg., July 31, tpmd250110.

Eloff, Lydia, Andrés Aranda-Díaz, Isobel Routledge, et al. 2025. “High Prevalence of Molecular Markers Associated with Artemisinin, Sulfadoxine, and Pyrimethamine Resistance in Northern Namibia.” Am. J. Trop. Med. Hyg., July 31, tpmd240870.

Furstenau, Tara N, Ryann Whealy, Skylar Timm, et al. 2025. “High-Throughput Targeted Amplicon Screening Tool for Characterizing Intrahost Diversity in Staphylococcus Aureus Directly from Sample.” Microb. Genom. 11 (June).

Katairo, Thomas, Victor Asua, Bienvenu Nsengimaana, et al. 2025. “Performance of Molecular Inversion Probe DR23K and Paragon MAD4HatTeR Amplicon Sequencing Panels for Detection of Plasmodium Falciparum Mutations Associated with Antimalarial Drug Resistance.” Res. Sq., January 21.

Makunin, Alex, Petra Korlević, Naomi Park, et al. 2021. “A Targeted Amplicon Sequencing Panel to Simultaneously Identify Mosquito Species and Plasmodium Presence Across the Entire Anopheles Genus.” Mol. Ecol. Resour., May 30.

Nhlengethwa, Nomcebo, Andrés Aranda-Díaz, Sibonakaliso Vilakati, et al. 2025. “Genomic Surveillance Reveals Clusters of Plasmodium Falciparum Antimalarial Resistance Markers in Eswatini, a Low-Transmission Setting.” medRxiv, July 31, 2025.07.30.25332463.

Raman, Jaishree, Maxwell Mabona, Qedusizi Nyawo, et al. 2025. “Very Low Prevalence of Validated kelch13 Mutations and Absence of hrp2/3 Double Gene Deletions in South African Malaria-Eliminating Districts (2022-2024).” medRxiv, April 1.

Tessema, Sofonias K, Nicholas J Hathaway, Noam B Teyssier, et al. 2022. “Sensitive, Highly Multiplexed Sequencing of Microhaplotypes from the Plasmodium Falciparum Heterozygome.” J. Infect. Dis. 225 (April): 1227–37.

Williamson, Charles H D, Adam J Vazquez, Amalee E Nunnally, et al. 2024. “ColiSeq: A Multiplex Amplicon Assay That Provides Strain Level Resolution of Escherichia Coli Directly from Clinical Specimens.” Microbiol. Spectr. 12 (June): e0413923.

--- title: PMO Examples --- {{< fa file >}} ```{r setup, echo=FALSE} source("../common.R") ``` <script src="https://code.jquery.com/jquery-2.2.2.min.js"></script> <script> $(document).ready(function() { document.querySelectorAll('.downloadLink').forEach(function(e) { e.setAttribute('download', e.text); }); document.querySelectorAll('.downloadLink').forEach(function(e) { e.innerHTML = '<i class="fa fa-download"></i> ' + e.text; }); }); </script> ## Minimum PMO example ### S_aureus Contains the PMO for the S. aureus dataset - Furstenau2025_PMO.json.gz. This PMO was contructed from SRA-sourced data[@Furstenau2025-bu] ```{r} #| results: asis #| echo: false cat(createDownloadLink("../pmo_example_datasets/S_aureus/minimum_Furstenau2025_PMO.json.gz")) ``` ## Example data from PMO manuscript ### ANOSPP Anopheles and Plasmodium data obtained from 4128 mosquito samples from Gabon that were sequenced as part of the ANOSPP (ANOpheles SPecies identification and Plasmodium detection) project[@Makunin2021-pg] ```{r} #| results: asis #| echo: false cat(createDownloadLink("../pmo_example_datasets/ANOSPP/anospp_pmo.json.gz")) ``` ### GENE8 Public genomic surveillance data of Plasmodium falciparum from four countries: Eswatini, Namibia, South Africa, and Zambia. This folder contains input files, intermediate PMOs, and processing notebooks [@Aranda-Diaz2025-vx][@Eloff2025-bs][@Nhlengethwa2025-tl][@Raman2025-dk] ```{r} #| results: asis #| echo: false cat(createDownloadLink("../pmo_example_datasets/GENE8/dataset1_pmo_qc_pass.json.gz")) ``` ### mips_v_mad4hatter Contains the PMO containing specimens that were sequenced using both the MAD4HatTeR amplicon sequencing and the DR23K molecular inversion probe (MIP) assay [@Katairo2025-vo] ```{r} #| results: asis #| echo: false cat(createDownloadLink("../pmo_example_datasets/mips_v_mad4hatter/PRJNA1252738_PMO.json.gz")) ``` ### E_coli Contains the PMO for the E. coli dataset - e_coli_coliseq_PMO.json.gz. This PMO was contructed from SRA-sourced data[@Williamson2024-uv] ```{r} #| results: asis #| echo: false cat(createDownloadLink("../pmo_example_datasets/E_coli/e_coli_coliseq_PMO.json.gz")) ``` ### S_aureus Contains the PMO for the S. aureus dataset - Furstenau2025_PMO.json.gz. This PMO was contructed from SRA-sourced data[@Furstenau2025-bu] ```{r} #| results: asis #| echo: false cat(createDownloadLink("../pmo_example_datasets/S_aureus/Furstenau2025_PMO.json.gz")) ``` ### Additional Example data format Example created from a study from Mozambique[@Tessema2022-fg] <https://academic.oup.com/jid/article/225/7/1227/5897005> ```{r} #| results: asis #| echo: false cat(createDownloadLink("moz2018_PMO.json.gz")) ``` #### From Pf7+ data for the same panel above Global data microhaplotypes were constructed by PathWeaver for the same targeted amplicon panel above. This includes approximately 1900 samples. ```{r} #| results: asis #| echo: false cat(createDownloadLink("PathWeaverHeome1_PMO.json.gz")) ```