Pathogen Informatics, Wellcome Sanger Institute's repositories
sh16_scripts
Deprecated scripts for reference only
software-tracker
API and helper scripts for the pathogen software installation tracking database
nextflow-commons
Store of generic templates and scripts for nextflow pipelines
TpRNAseq
A bacterial RNAseq pipeline, designed for analysis of Treponema pallidum data
bentley-app
Static site for Stephen Bentley's group
bactgen-training-app
Static site for training on the Juno/GPS2 projects
paminfo-training-FE
A lightweight frontend application used for testing applicants
external-import
Import external data into our tracking databases
Bio-Tradis
A set of tools to analyse the output from TraDIS analyses
assembly-stats
Get assembly statistics from FASTA and FASTQ files
multimapper
Updated conversions of Simon Harris' pipelines
Bio-AutomatedAnnotation
Perl module to take in an genomic assembly and produce annoation
vr-codebase
The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute
update_pipeline
Update a pipelines metadata