Pathogen Genomics, Wellcome Trust Sanger Institute
Validate a genome metadata manifest against a checklist
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Using kmers to find plasmids
Rapid large-scale prokaryote pan genome analysis
vr-codebase
Forked from VertebrateResequencing/vr-codebaseThe overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute
Finds SNP sites from a multi-FASTA alignment file
DBIC schema for the sequencescape warehouse database
DBIC schema for pathogens tracking databases
Improve the quality of a denovo assembly by scaffolding and gap filling
A set of tools to analyse the output from TraDIS analyses
Python3 package to handle job submission to a compute farm
Antimicrobial Resistance Identification By Assembly
tracer
Forked from Teichlab/tracerTraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
To build a virtual machine with some Sanger pathogens software installed
Web interface for Companion
Takes a jinja2 template and some json and sends an email
Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
de novo virus assembler of Illumina paired reads
Python3 module for running MUMmer and reading the output
Python3 scripts to manipulate FASTA and FASTQ files
A tool to circularize genome assemblies
Python interface for reading and converting EuPathDB flat file dumps
Website to show your team's publications (which are in PubMed)
andrewjpage
simonrharris