Featured Repos

Other Repos

Repository Description Score
circlator A tool to circularize genome assemblies 42.603
iva de novo virus assembler of Illumina paired reads 42.323
gubbins Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins 40.933
plasmidtron Assembling the cause of phenotypes and genotypes from NGS data 4.38
snp-sites Finds SNP sites from a multi-FASTA alignment file 3.999
companion Pipeline for automatic eukaryotic parasite annotation 3.679
gff3toembl Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI 3.662
saffrontree SaffronTree: Reference free rapid phylogenetic tree construction from raw read data 3.528
Fastaq Python3 scripts to manipulate FASTA and FASTQ files 3.51
panito Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment 3.46
Bio-Tradis A set of tools to analyse the output from TraDIS analyses 3.239
assembly_improvement Improve the quality of a denovo assembly by scaffolding and gap filling 3.102
GeneDB Web front-end for genomic data, developed at the Pathogen Genomics group, Wellcome Trust Sanger Institute 2.979
ntd_website Wellcome Sanger Institute NTD website 2.913
pymummer Python3 module for running MUMmer and reading the output 2.901
MIDAS Front end for the HICF pathogen genome store 2.688
mlst_check Multilocus sequence typing by blast using the schemes from PubMLST 2.684
krocus Predict MLST directly from uncorrected long reads 2.595
assembly-stats Get assembly statistics from FASTA and FASTQ files 2.474
pathogens-vm To build a virtual machine with some Sanger pathogens software installed 2.37
SnpEffWrapper Takes a VCF and applies annotations from a GFF using SnpEff 2.339
update_pipeline None 2.184
phandango an interactive viewer for populations of bacterial genomes linked by a phylogeny 2.023
jobTree Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor) 2.002
progressiveCactus Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules 2.001
sanger-pathogens.github.io Summary of Sanger Pathogen's Repos 1.975
pathogen-informatics-training None 1.96
Web-Artemis None 1.875
GithubConglomerate Brings together details of github repos across organisations 1.703
deago None 1.647
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) 1.381
Bio-Metadata-Validator Validate a genome metadata manifest against a checklist 1.207
chado-export Script for exporting organism sequences from a CHADO database to GFF file. 1.028
ariba-publication Supplementary data and scripts for ARIBA publication 1.002
Bio-Sequencescape-Schema DBIC schema for the sequencescape warehouse database 1.0
Bio-Track-Schema DBIC schema for pathogens tracking databases 1.0
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
structure Copy of Structure 2.3.4 with patch applied to fix seg fault 1.0
Bio-ReferenceManager None 0.995
seroba None 0.711
Bio-Deago None 0.522
Bio-Metagenomics None 0.434
vr-codebase The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute 0.391
crawl2 A spiritual successor to Crawl 0.345
Bio-RNASeq The new Sanger Pathogen Informatics RNA Seq analysis pipeline 0.298
Farmpy Python3 package to handle job submission to a compute farm 0.282
deployment None 0.252
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
setup_tracking setup a vrtracking pipeline 0.18
Bio-AutomatedAnnotation Perl module to take in an genomic assembly and produce annoation 0.143
pipelines_reporting None 0.138
reference_track None 0.137
find_files_for_deletion None 0.137
Farm_blast Python3 module to run blast+ or blastall in parallel on an LSF compute farm 0.122
PathPipeConfTools Outputs details of all of the pathogen jobs in the pipeline 0.121
Bio-Path-Find None 0.109
iva-publication Supplementary scripts and data for the IVA publication 0.1
Bio-InterProScanWrapper None 0.098
Bio-ENA-DataSubmission None 0.029
Bio-VertRes-Config None 0.014
Bio-HICF-Schema None 0.011
remove_blocks_from_aln None 0.001
madansi None 0.0
orderedPainting None 0.0
Bio-VertRes-Permissions None 0.0
HICF_checklist None 0.0

Data collected: 2018-04-23T19:07:40Z