ArticleBMC bioinformatics2014
Identification of pathogen genomic variants through an integrated pipeline.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
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- Reaction hijacking inhibition of Plasmodium falciparum asparagine tRNA synthetase.Nature communications · 2024Article
- Direct long read visualization reveals metabolic interplay between two antimalarial drug targets.bioRxiv : the preprint server for biology · 2023Article
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- Cytoplasmic isoleucyl tRNA synthetase as an attractive multistage antimalarial drug target.Science translational medicine · 2023Article
- Resolving drug selection and migration in an inbred South American Plasmodium falciparum population with identity-by-descent analysis.PLoS pathogens · 2022Article
- Reaction hijacking of tyrosine tRNA synthetase as a new whole-of-life-cycle antimalarial strategy.Science (New York, N.Y.) · 2022Article
- The Plasmodium falciparum ABC transporter ABCI3 confers parasite strain-dependent pleiotropic antimalarial drug resistance.Cell chemical biology · 2022Article
- Associations between Varied Susceptibilities to PfATP4 Inhibitors and Genotypes in Ugandan Plasmodium falciparum Isolates.Antimicrobial agents and chemotherapy · 2021Article
- PfMFR3: A Multidrug-Resistant Modulator inACS infectious diseases · 2021Article
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- Human Aurora kinase inhibitor Hesperadin reveals epistatic interaction between Plasmodium falciparum PfArk1 and PfNek1 kinases.Communications biology · 2020Article
- The mutation of a PECTATE LYASE-LIKE gene is responsible for the Yellow Margin phenotype in potato.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Covalent Plasmodium falciparum-selective proteasome inhibitors exhibit a low propensity for generating resistance in vitro and synergize with multiple antimalarial agents.PLoS pathogens · 2019Article
- Complex DNA structures trigger copy number variation across the Plasmodium falciparum genome.Nucleic acids research · 2019Article
- Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing.Genome medicine · 2018Article
- Analysis of Theileria orientalis draft genome sequences reveals potential species-level divergence of the Ikeda, Chitose and Buffeli genotypes.BMC genomics · 2018Article
- Mutations in the pantothenate kinase of Plasmodium falciparum confer diverse sensitivity profiles to antiplasmodial pantothenate analogues.PLoS pathogens · 2018Article
- Hexahydroquinolines are antimalarial candidates with potent blood-stage and transmission-blocking activity.Nature microbiology · 2017Article
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9 authors.
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Abstract
backgroundWhole-genome sequencing represents a powerful experimental tool for pathogen research. We present methods for the analysis of small eukaryotic genomes, including a streamlined system (called Platypus) for finding single nucleotide and copy number variants as well as recombination events.
resultsWe have validated our pipeline using four sets of Plasmodium falciparum drug resistant data containing 26 clones from 3D7 and Dd2 background strains, identifying an average of 11 single nucleotide variants per clone. We also identify 8 copy number variants with contributions to resistance, and report for the first time that all analyzed amplification events are in tandem.
conclusionsThe Platypus pipeline provides malaria researchers with a powerful tool to analyze short read sequencing data. It provides an accurate way to detect SNVs using known software packages, and a novel methodology for detection of CNVs, though it does not currently support detection of small indels. We have validated that the pipeline detects known SNVs in a variety of samples while filtering out spurious data. We bundle the methods into a freely available package.
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