Portable Microhaplotype Object (PMO)Portable Microhaplotype Object (PMO) Portable Microhaplotype Object (PMO)
  • Home
  • Format Info
    • Overview of Format

    • PMO fields overview
    • PMO within a Data Analysis Ecosystem
    • History of Format Development

    • History of how PMO Format was derived
    • Overview of Format For Bioinformaticians

    • PMO Examples
    • Format Overview For Developers
  • PMO App
  • pmotools-python
    • Overview
    • Installation
    • Manual
    • Python Interface Tutorials
    • Building a PMO with minimum required fields
    • Updating the Specimen Meta Information in a minimum PMO
    • Building a PMO including optional sections and fields
    • Getting basic information from a PMO file
    • Command line Interface Tutorials
    • Command line interface guide
    • Extracting allele tables from a PMO
    • Subsetting a PMO
    • Getting basic information from a PMO
    • Extracting panel info from PMO
    • Handling Multiple PMOs
    • Validating PMO files
  • Resources
    • References
    • Documentation
    • Documentation Source Code
    • Comment or Report an issue for Documentation

    • pmotools-python
    • pmotools-python Source Code
    • Comment or Report an issue for pmotools-python

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.
Aranda-Díaz, Andrés, Eric Neubauer Vickers, Kathryn Murie, et al. 2025. “Sensitive and Modular Amplicon Sequencing of Plasmodium Falciparum Diversity and Resistance for Research and Public Health.” Sci. Rep. 15 (March): 10737.
Crystal-Ornelas, Robert, Charuleka Varadharajan, Dylan O’Ryan, et al. 2022. “Enabling FAIR Data in Earth and Environmental Science with Community-Centric (Meta)data Reporting Formats.” Sci Data 9 (1): 700.
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).
Jacob, Christopher G, Nguyen Thuy-Nhien, Mayfong Mayxay, et al. 2021. “Genetic Surveillance in the Greater Mekong Subregion and South Asia to Support Malaria Control and Elimination.” Elife 10 (August).
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.
Kattenberg Johanna Helena, Fernandez-Miñope Carlos, van Dijk Norbert J., et al. 2023. “Malaria Molecular Surveillance in the Peruvian Amazon with a Novel Highly Multiplexed Plasmodium Falciparum AmpliSeq Assay.” Microbiology Spectrum 0 (0): e00960–22.
LaVerriere, Emily, Philipp Schwabl, Manuela Carrasquilla, et al. 2022. “Design and Implementation of Multiplexed Amplicon Sequencing Panels to Serve Genomic Epidemiology of Infectious Disease: A Malaria Case Study.” Mol. Ecol. Resour. 22 (6): 2285–303.
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.
Oldoni, Fabio, Kenneth K Kidd, and Daniele Podini. 2019. “Microhaplotypes in Forensic Genetics.” Forensic Sci. Int. Genet. 38 (January): 54–69.
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.
Sadler, Jacob M, Alfred Simkin, Valery P K Tchuenkam, et al. 2024. “Application of a New Highly Multiplexed Amplicon Sequencing Tool to Evaluate Plasmodium Falciparum Antimalarial Resistance and Relatedness in Individual and Pooled Samples from Dschang, Cameroon.” Front. Parasitol. 3: 1509261.
SRA Metadata and Submission Overview. n.d. Https://www.ncbi.nlm.nih.gov/sra/docs/submitmeta/.
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.
Vangay Pajau, Burgin Josephine, Johnston Anjanette, et al. 2021. “Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities.” mSystems 6 (1): e01194–20.
Weisenhorn, Pamela, and Kathleen Beilsmith. 2022. ESS-DIVE Reporting Format for Amplicon Abundance Table. Environmental System Science Data Infrastructure for a Virtual Ecosystem; Environmental Systems Science Data Infrastructure for a Virtual Ecosystem (ESS-DIVE).
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.
Yilmaz, Pelin, Renzo Kottmann, Dawn Field, et al. 2011. “Minimum Information about a Marker Gene Sequence (MIMARKS) and Minimum Information about Any (x) Sequence (MIxS) Specifications.” Nat. Biotechnol. 29 (5): 415–20.
Source Code
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title: References
nocite: |
  @*
---

```{r setup, echo=FALSE, message=FALSE}
source("common.R")
```



::: {#refs}

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