Pathogen Informatics, Wellcome Sanger Institute

Summary of Sanger Pathogen's Repos

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

Perl module to take in an genomic assembly and produce annoation

Tools for accessing CHADO databases.

Finds SNP sites from a multi-FASTA alignment file

Pipeline for automatic eukaryotic parasite annotation

To build a virtual machine with some Sanger pathogens software installed

Munges GFF3 files exported from Chado (http://www.gmod.org/) database to make them suitable for loading into WebApollo.

Conda recipes for the sanger-pathogens channel: https://anaconda.org/sanger-pathogens

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

A set of tools to analyse the output from TraDIS analyses

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

A tool to circularize genome assemblies

Rapid large-scale prokaryote pan genome analysis

Antimicrobial Resistance Identification By Assembly

de novo virus assembler of Illumina paired reads

A Python application for exporting organism sequences from a CHADO database to GFF file.

Takes a VCF and applies annotations from a GFF using SnpEff

A spiritual successor to Crawl

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Assembling the cause of phenotypes and genotypes from NGS data

Update a pipelines metadata