Computational protocol: Whole Genome Analysis of Injectional Anthrax Identifies Two Disease Clusters Spanning More Than 13 Years

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Protocol publication

[…] Reference genome assemblies were downloaded from GenBank (). Paired-end reads were aligned against the Ames Ancestor genome (NC_007530) using BWA-MEM () and SNPs were called with the UnifiedGenotyper method in GATK (, ); any SNPs that had a coverage less than 6X depth and majority allele frequencies < 90% were discarded. The reference (Ames Ancestor) was aligned against itself with NUCmer () and SNPs that fell into regions that mapped more than once were removed from the analysis. External genome assemblies were aligned against the Ames Ancestor genome with nucmer and a direct one-to-one mapping was generated to identify variant as well as invariant sites (). All of these methods are wrapped by the Northern Arizona SNP Pipeline (NASP; https://github.com/TGenNorth/NASP). Phylogenetic analysis was performed by maximum parsimony analysis using MEGA 6.0 (). […]

Pipeline specifications

Software tools BWA, GATK, MUMmer, NASP, MEGA
Applications WGS analysis, Nucleotide sequence alignment
Organisms Bacillus anthracis, Homo sapiens
Chemicals Heroin