Featured Repos

Other Repos

Repository Description Score
circlator A tool to circularize genome assemblies 46.053
iva de novo virus assembler of Illumina paired reads 45.568
gubbins Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins 44.27
snp-sites Finds SNP sites from a multi-FASTA alignment file 4.328
Fastaq Python3 scripts to manipulate FASTA and FASTQ files 4.18
gff3toembl Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI 3.664
Bio-Tradis A set of tools to analyse the output from TraDIS analyses 3.419
assembly_improvement Improve the quality of a denovo assembly by scaffolding and gap filling 3.243
GeneDB Web front-end for genomic data, developed at the Pathogen Genomics group, Wellcome Trust Sanger Institute 3.16
plasmidtron Using kmers to find plasmids 2.995
companion Pipeline for automatic eukaryotic parasite annotation 2.961
pymummer Python3 module for running MUMmer and reading the output 2.887
saffrontree SaffronTree: Reference free rapid phylogenetic tree construction from raw read data 2.874
panito Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment 2.811
mlst_check Multilocus sequence typing by blast using the schemes from PubMLST 2.792
ntd_website Wellcome Sanger Institute NTD website 2.748
assembly-stats Get assembly statistics from FASTA and FASTQ files 2.622
update_pipeline None 2.484
deago None 2.455
pathogens-vm To build a virtual machine with some Sanger pathogens software installed 2.207
phandango an interactive viewer for populations of bacterial genomes linked by a phylogeny 2.054
jobTree Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor) 2.004
progressiveCactus Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules 2.002
sanger-pathogens.github.io Summary of Sanger Pathogen's Repos 1.976
MIDAS Front end for the HICF pathogen genome store 1.951
Web-Artemis None 1.875
SnpEffWrapper Takes a VCF and applies annotations from a GFF using SnpEff 1.685
json2email Takes a jinja2 template and some json and sends an email 1.577
citation_reporter Website to show your team's publications (which are in PubMed) 1.396
pathogen-informatics-training None 1.247
Bio-Metadata-Validator Validate a genome metadata manifest against a checklist 1.208
chado-export Script for exporting organism sequences from a CHADO database to GFF file. 1.065
ariba-publication Supplementary data and scripts for ARIBA publication 1.005
Bio-Sequencescape-Schema DBIC schema for the sequencescape warehouse database 1.001
Bio-Track-Schema DBIC schema for pathogens tracking databases 1.001
Bio-PacbioMethylation Runs Pacbio methylation pipeline 1.0
companion-publication Accompanying information for the Companion publication 1.0
PySnpSites Experiments optimising python (with Cython) 1.0
ABACAS2 ABACAS2, a tool for ordering and orientating biosequences along a reference 1.0
FMAP Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies 1.0
fastqcheck Generate statistics on and validate fastq files 1.0
phandangoExampleData The data underlying the examples on https://jameshadfield.github.io/phandango 1.0
GithubConglomerate Brings together details of github repos across organisations 1.0
structure Copy of Structure 2.3.4 with patch applied to fix seg fault 1.0
Bio-Deago None 0.978
seroba None 0.89
Bio-Metagenomics None 0.735
vr-codebase The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute 0.363
crawl2 A spiritual successor to Crawl 0.275
Farmpy Python3 package to handle job submission to a compute farm 0.263
deployment None 0.254
Bio-RNASeq The new Sanger Pathogen Informatics RNA Seq analysis pipeline 0.221
setup_tracking setup a vrtracking pipeline 0.21
annot-web Web interface for Companion 0.2
kraken Kraken taxonomic sequence classification system 0.2
fastml Addtional functionality for fastml, see http://fastml.tau.ac.il 0.2
Bio-AutomatedAnnotation Perl module to take in an genomic assembly and produce annoation 0.173
pipelines_reporting None 0.14
reference_track None 0.137
find_files_for_deletion None 0.137
Bio-Path-Find None 0.124
Farm_blast Python3 module to run blast+ or blastall in parallel on an LSF compute farm 0.123
PathPipeConfTools Outputs details of all of the pathogen jobs in the pipeline 0.123
iva-publication Supplementary scripts and data for the IVA publication 0.1
Bio-ENA-DataSubmission None 0.041
Bio-VertRes-Config None 0.032
Bio-HICF-Schema None 0.026
Bio-InterProScanWrapper None 0.021
Bio-ReferenceManager None 0.002
remove_blocks_from_aln None 0.002
madansi None 0.0
orderedPainting None 0.0
Bio-VertRes-Permissions None 0.0
HICF_checklist None 0.0

Data collected: 2018-03-20T20:07:41Z