Featured Repos

Other Repos

Repository Description Score
ariba Antimicrobial Resistance Identification By Assembly 51.522
gubbins Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins 45.553
iva de novo virus assembler of Illumina paired reads 41.738
Bio-Tradis A set of tools to analyse the output from TraDIS analyses 4.377
Fastaq Python3 scripts to manipulate FASTA and FASTQ files 4.143
snp-sites Finds SNP sites from a multi-FASTA alignment file 3.694
gff3toembl Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI 3.693
assembly-stats Get assembly statistics from FASTA and FASTQ files 3.601
plasmidtron Using kmers to find plasmids 3.155
assembly_improvement Improve the quality of a denovo assembly by scaffolding and gap filling 3.0
pymummer Python3 module for running MUMmer and reading the output 2.96
companion Pipeline for automatic eukaryotic parasite annotation 2.941
GeneDB Web front-end for genomic data, developed at the Pathogen Genomics group, Wellcome Trust Sanger Institute 2.806
panito Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment 2.725
mlst_check Multilocus sequence typing by blast using the schemes from PubMLST 2.608
saffrontree SaffronTree: Reference free rapid phylogenetic tree construction from raw read data 2.608
phandango an interactive viewer for populations of bacterial genomes linked by a phylogeny 2.55
pathogens-vm To build a virtual machine with some Sanger pathogens software installed 2.211
update_pipeline None 2.118
jobTree Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor) 2.039
progressiveCactus Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules 2.018
sanger-pathogens.github.io Summary of Sanger Pathogen's Repos 1.976
MIDAS Front end for the HICF pathogen genome store 1.955
Web-Artemis None 1.879
pathogen-informatics-training None 1.795
SnpEffWrapper Takes a VCF and applies annotations from a GFF using SnpEff 1.689
chado-export Script for exporting organism sequences from a CHADO database to GFF file. 1.668
citation_reporter Website to show your team's publications (which are in PubMed) 1.637
json2email Takes a jinja2 template and some json and sends an email 1.581
seroba None 1.482
Bio-Metadata-Validator Validate a genome metadata manifest against a checklist 1.219
ariba-publication Supplementary data and scripts for ARIBA publication 1.056
ntd_website WTSI NTD website 1.017
Bio-Sequencescape-Schema DBIC schema for the sequencescape warehouse database 1.009
Bio-Track-Schema DBIC schema for pathogens tracking databases 1.006
Bio-PacbioMethylation Runs Pacbio methylation pipeline 1.005
companion-publication Accompanying information for the Companion publication 1.005
PySnpSites Experiments optimising python (with Cython) 1.004
ABACAS2 ABACAS2, a tool for ordering and orientating biosequences along a reference 1.004
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
structure Copy of Structure 2.3.4 with patch applied to fix seg fault 1.0
vr-codebase The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute 0.35
Bio-Deago None 0.341
Farmpy Python3 package to handle job submission to a compute farm 0.285
crawl2 A spiritual successor to Crawl 0.275
Bio-HICF-Schema None 0.266
deployment None 0.234
deago None 0.23
Bio-RNASeq The new Sanger Pathogen Informatics RNA Seq analysis pipeline 0.221
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
pipelines_reporting None 0.168
Farm_blast Python3 module to run blast+ or blastall in parallel on an LSF compute farm 0.144
PathPipeConfTools Outputs details of all of the pathogen jobs in the pipeline 0.14
setup_tracking setup a vrtracking pipeline 0.137
reference_track None 0.137
find_files_for_deletion None 0.137
Bio-Path-Find None 0.131
iva-publication Supplementary scripts and data for the IVA publication 0.1
Bio-AutomatedAnnotation Perl module to take in an genomic assembly and produce annoation 0.1
Bio-ENA-DataSubmission None 0.031
Bio-InterProScanWrapper None 0.024
Bio-ReferenceManager None 0.02
remove_blocks_from_aln None 0.019
Bio-VertRes-Config None 0.011
Bio-Metagenomics None 0.005
madansi None 0.004
orderedPainting None 0.0
Bio-VertRes-Permissions None 0.0
HICF_checklist None 0.0

Data collected: 2017-12-16T20:07:59Z