14 projects
wgscovplot
Create interactive comparative sequencing coverage plots from virus sequencing data.
miso-tool
A tool to work with sequencing run and sample info from MISO LIMS Pinery JSON data
xlavir
Excel report from viral sequencing analysis output
gfflu
Annotate Influenza A virus gene segment sequences and output GFF3 files.
sistr-cmd
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
Generate a standalone HTML file with an interactive phylogenetic tree using PhyloCanvas
bio-hansel
Subtype microbial whole-genome sequencing (WGS) data using SNV targeting k-mer subtyping schemes.
refseq-masher
Mash MinHash search your sequences against a NCBI RefSeq genomes database
filter-classified-reads
Filter for reads from taxa of interest using Kraken2/Centrifuge classification results
viral-verify
viralVerify rewrite/refactor for PyPI packaging and distribution
blast2xl
BLAST output to XLSX spreadsheet
vcf-consensus-builder
Build a consensus sequence from a VCF and ref sequence masking low and no coverage positions.
enteritidis-subtyping
Subtype Salmonella Enteritidis genomes using a 33bp k-mer typing scheme
heidelberg-subtyping
Subtype Salmonella Heidelberg genomes using a 33bp k-mer typing scheme