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abacas2

ABACAS2, a tool for ordering and orientating biosequences along a reference

annot-web

Web interface for Companion

annotations_update

archive_project

Tool to back up the data produced by the Pathogen Informatics sequencing pipelines to an S3 server

ariba

Antimicrobial Resistance Identification By Assembly

ariba-publication

Supplementary data and scripts for ARIBA publication

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-stats

Get assembly statistics from FASTA and FASTQ files

assembly_improvement

Improve the quality of a denovo assembly by scaffolding and gap filling

assembly_tools

Scripts relating to genome assemblies

bact-gen-scripts

baker

A tool to generate configuration files and wrapper scripts

bio-automatedannotation

Perl module to take in an genomic assembly and produce annoation

bio-dbannotationremapper

Relocate annotation in a database based on flat files (embl)

bio-deago

bio-ena-datasubmission

bio-hicf-schema

bio-interproscanwrapper

bio-metadata-validator

Validate a genome metadata manifest against a checklist

bio-metagenomics

bio-pacbiomethylation

Runs Pacbio methylation pipeline

bio-path-find

bio-pipeline-comparison

bio-referencemanager

bio-retrieveassemblies

bio-rnaseq

The new Sanger Pathogen Informatics RNA Seq analysis pipeline

bio-sequencescape-schema

DBIC schema for the sequencescape warehouse database

bio-track-schema

DBIC schema for pathogens tracking databases

bio-tradis

A set of tools to analyse the output from TraDIS analyses

bio-vertres-config