Peter Kruczkiewicz

miso-tool

Last released Apr 26, 2024

A tool to work with sequencing run and sample info from MISO LIMS Pinery JSON data

wgscovplot

Last released Feb 20, 2024

Create interactive comparative sequencing coverage plots from virus sequencing data.

xlavir

Last released Dec 6, 2023

Excel report from viral sequencing analysis output

gfflu

Last released Aug 9, 2023

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

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