Wellcome Sanger Institute

Update of multiple_mappings_to_bam.py pipeline

Artemis is a free genome viewer and annotation tool.

A dependency docker image for the GBS Typer pipeline.

de novo virus assembler of Illumina paired reads http://sanger-pathogens.github.io/iva/

Gubbins

Get assembly statistics from FASTA and FASTQ files.

A python3 tool for validating taxonomy identification on sequencing manifests to NCBI standards

SampleVcfToZarr docker image dependency for the malaria pipelines

GATK3 docker image dependency for the malaria pipelines

mask, remove or keep regions in an alignment

A set of bioinformatics training courses

ARIBA: Antibiotic Resistance Identification By Assembly

Picard docker image dependency for the malaria pipelines

Samtools docker image dependency for the malaria pipelines

BWA docker image dependency for the malaria pipelines

Biobambam docker image dependency for the malaria pipelines

lftp docker image dependency for the malaria pipelines

Tools for accessing CHADO databases

A tool to circularize genome assemblies http://sanger-pathogens.github.io/circlator/

A python3 library to parse external import spreadsheets

Rapid high throughput serotyping of Streptococcus pneumoniae from WGS data

Roary the bacterial pan-genome pipeline

A set of tools to analyse the output from TraDIS analyses.