Featured Repos

Other Repos

Repository Description Score
circlator A tool to circularize genome assemblies 47.201
gubbins Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins 47.056
iva de novo virus assembler of Illumina paired reads 40.572
snp-sites Finds SNP sites from a multi-FASTA alignment file 4.462
Bio-Tradis A set of tools to analyse the output from TraDIS analyses 4.132
plasmidtron Using kmers to find plasmids 4.082
ntd_website Wellcome Sanger Institute NTD website 3.921
assembly_improvement Improve the quality of a denovo assembly by scaffolding and gap filling 3.868
GeneDB Web front-end for genomic data, developed at the Pathogen Genomics group, Wellcome Trust Sanger Institute 3.723
gff3toembl Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI 3.669
saffrontree SaffronTree: Reference free rapid phylogenetic tree construction from raw read data 3.458
assembly-stats Get assembly statistics from FASTA and FASTQ files 3.443
Fastaq Python3 scripts to manipulate FASTA and FASTQ files 3.395
mlst_check Multilocus sequence typing by blast using the schemes from PubMLST 3.376
companion Pipeline for automatic eukaryotic parasite annotation 2.939
pymummer Python3 module for running MUMmer and reading the output 2.894
panito Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment 2.714
pathogen-informatics-training None 2.417
phandango an interactive viewer for populations of bacterial genomes linked by a phylogeny 2.22
pathogens-vm To build a virtual machine with some Sanger pathogens software installed 2.208
jobTree Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor) 2.015
progressiveCactus Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules 2.007
sanger-pathogens.github.io Summary of Sanger Pathogen's Repos 1.976
MIDAS Front end for the HICF pathogen genome store 1.952
update_pipeline None 1.928
Web-Artemis None 1.877
SnpEffWrapper Takes a VCF and applies annotations from a GFF using SnpEff 1.687
json2email Takes a jinja2 template and some json and sends an email 1.578
citation_reporter Website to show your team's publications (which are in PubMed) 1.477
seroba None 1.463
chado-export Script for exporting organism sequences from a CHADO database to GFF file. 1.267
Bio-Metadata-Validator Validate a genome metadata manifest against a checklist 1.211
ariba-publication Supplementary data and scripts for ARIBA publication 1.022
Bio-Sequencescape-Schema DBIC schema for the sequencescape warehouse database 1.004
Bio-Track-Schema DBIC schema for pathogens tracking databases 1.002
Bio-PacbioMethylation Runs Pacbio methylation pipeline 1.002
companion-publication Accompanying information for the Companion publication 1.002
PySnpSites Experiments optimising python (with Cython) 1.002
ABACAS2 ABACAS2, a tool for ordering and orientating biosequences along a reference 1.002
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-Deago None 0.991
vr-codebase The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute 0.387
crawl2 A spiritual successor to Crawl 0.275
Farmpy Python3 package to handle job submission to a compute farm 0.27
setup_tracking setup a vrtracking pipeline 0.225
Bio-RNASeq The new Sanger Pathogen Informatics RNA Seq analysis pipeline 0.221
deployment None 0.212
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-Path-Find None 0.197
pipelines_reporting None 0.149
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 0.13
PathPipeConfTools Outputs details of all of the pathogen jobs in the pipeline 0.128
Bio-HICF-Schema None 0.107
Bio-ENA-DataSubmission None 0.104
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-VertRes-Config None 0.099
deago None 0.092
Bio-InterProScanWrapper None 0.022
Bio-ReferenceManager None 0.008
remove_blocks_from_aln None 0.008
Bio-Metagenomics None 0.002
madansi None 0.002
orderedPainting None 0.0
Bio-VertRes-Permissions None 0.0
HICF_checklist None 0.0

Data collected: 2018-01-22T20:07:37Z