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ensembl-production

Ensembl Production code

ensembl-production-imported

Production pipelines used by data-teams to process imported genomes (former EnsemblGenomes pipelines)

ensembl-static-1

Stores all static contents for Non-vertebrates divisions and species.

fastaq

Python3 scripts to manipulate FASTA and FASTQ files

find_files_for_deletion

gap5_consistency_checker

genedb

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

github3.py

Python library for interfacing with the GitHub APIv3

lsf_jobrunner_roary

midas

Front end for the HICF pathogen genome store

mlst_check

pathfind

Modularised versions of *find scripts

pipelines_reporting

project-track

Track information about sequencing projects using ecap database

public-plugins

Plugins for an Ensembl website

pymummer

Python3 module for running MUMmer and reading the output

reference_track

roary

Rapid large-scale prokaryote pan genome analysis

sarscov2-annotation

Selection of code used to import SARS-CoV-2 related annotation into a BigBed file for loading into various genome browsers. This is based on efforts by the UCSC Genome Browser team

setup_tracking

setup a vrtracking pipeline

update_pipeline

validate_tools

File validation scripts and tools

vr-codebase

The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute

vr-pipe

Generic pipeline system

vrtrack_crawl