Computational protocol: In Vitro Resistance Selections for Plasmodium falciparum Dihydroorotate Dehydrogenase Inhibitors Give Mutants with Multiple Point Mutations in the Drug-binding Site and Altered Growth*

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Protocol publication

[…] Sequenced reads were aligned against the P. falciparum 3D7 reference from PlasmoDB (version 7.1*) () using BWA version 0.5.7 (). Duplicate reads were marked using Picard MarkDuplicates. Consensus bases were called using the Genome Analysis Toolkit (GATK) Unified Genotyper (version 1.0.5974) () and the SAMtools (version 0.1.16) () mpileup command. Only bases that were called as homozygous for the reference or the alternate allele with a genotype quality of at least 30 was considered. […]

Pipeline specifications

Software tools BWA, Picard, GATK, SAMtools
Databases PlasmoDB
Application WGS analysis
Organisms Plasmodium falciparum, Homo sapiens
Diseases Infection, Malaria