Peter Kruczkiewicz

gfflu

Last released Aug 9, 2023

Annotate Influenza A virus gene segment sequences and output GFF3 files.

xlavir

Last released May 19, 2023

Excel report from viral sequencing analysis output

sistr-cmd

Last released Feb 9, 2023

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.

shiptv

Last released May 13, 2021

Generate a standalone HTML file with an interactive phylogenetic tree using PhyloCanvas

bio-hansel

Last released Mar 5, 2021

Subtype microbial whole-genome sequencing (WGS) data using SNV targeting k-mer subtyping schemes.

refseq-masher

Last released Nov 23, 2020

Mash MinHash search your sequences against a NCBI RefSeq genomes database

filter-classified-reads

Last released Sep 17, 2020

Filter for reads from taxa of interest using Kraken2/Centrifuge classification results

viral-verify

Last released Jun 4, 2020

viralVerify rewrite/refactor for PyPI packaging and distribution

blast2xl

Last released Jan 31, 2020

BLAST output to XLSX spreadsheet

vcf-consensus-builder

Last released Jan 3, 2020

Build a consensus sequence from a VCF and ref sequence masking low and no coverage positions.

enteritidis-subtyping

Last released Jul 25, 2017

Subtype Salmonella Enteritidis genomes using a 33bp k-mer typing scheme

heidelberg-subtyping

Last released Jul 17, 2017

Subtype Salmonella Heidelberg genomes using a 33bp k-mer typing scheme