aslett1

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

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

GeneDB

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

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

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

project-track

Track information about sequencing projects using ecap database

QUASR

reference_track

setup_tracking

setup a vrtracking pipeline

snp_sites

Finds SNP sites from a multi fasta alignment file