Excel report from viral sequencing analysis output
Generate a standalone HTML file with an interactive phylogenetic tree using PhyloCanvas
Subtype microbial whole-genome sequencing (WGS) data using SNV targeting k-mer subtyping schemes.
Mash MinHash search your sequences against a NCBI RefSeq genomes database
Filter for reads from taxa of interest using Kraken2/Centrifuge classification results
viralVerify rewrite/refactor for PyPI packaging and distribution
Serovar predictions from Salmonella whole-genome sequence assemblies by determination of antigen geneand cgMLST gene alleles using BLAST. Mash MinHash can also be used for serovar prediction.
BLAST output to XLSX spreadsheet
Build a consensus sequence from a VCF and ref sequence masking low and no coverage positions.
Subtype Salmonella Enteritidis genomes using a 33bp k-mer typing scheme
Subtype Salmonella Heidelberg genomes using a 33bp k-mer typing scheme