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ariba

Antibiotic Resistance Identification By Assembly

artemis

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

assembly_improvement

bio-automatedannotation

Perl module to take in an genomic assembly and produce annoation

bio-ena-datasubmission

bio-hicf-schema

bio-interproscanwrapper

bio-metadata-validator

Validate a genome metadata manifest against a checklist

bio-retrieveassemblies

bio-rnaseq

The new Sanger Pathogen Informatics RNA Seq analysis pipeline

bio-typinggenerator

bio-vertres-config

biopericles

A work in progress. BioPericles is designed to use supervised Machine Learning techniques to classify samples into clusters

bowtie2

bowtie2 test docker

circlator

A tool to circularize genome assemblies

citation_reporter

Website to show your team's publications (which are in PubMed)

concordance

deployment

farm_blast

Python3 module to run blast+ or blastall in parallel on an LSF compute farm

find_files_for_deletion

genedb

Web front-end for genomic data, developed at the Pathogen Genomics group, Wellcome Trust Sanger Institute

gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

hicf_checklist

json2email

Takes a jinja2 template and some json and sends an email

midas

Front end for the HICF pathogen genome store

mlst_check

pathfind

Modularised versions of *find scripts

pathogens-vm

To build a virtual machine with some Sanger pathogens software installed

pathpipeconftools

Outputs details of all of the pathogen jobs in the pipeline

pipelines_reporting