vsnpdev (pypi): USDA APHIS Veterinary Services (VS) Mycobacterium tuberculosis complex, mainly M. bovis, and Brucella sp. SNP pipeline. Genotyping from whole genome sequence (WGS) outputting BAM, VCF, SNP tables and phylogentic trees.
Keywords: analysis-pipeline|bam-files|brucella|freebayes|genomics|high|high-throughput-sequencing|mycobacterium-tuberculosis-complex|phylogenetics|pipeline|snp|snps|tuberculosis|vcf|wgs|whole-genome-sequencing