Featured Repos

Other Repos

Repository Description Score
circlator A tool to circularize genome assemblies 47.06
gubbins Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins 45.782
iva de novo virus assembler of Illumina paired reads 43.23
gff3toembl Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI 3.722
snp-sites Finds SNP sites from a multi-FASTA alignment file 3.701
pymummer Python3 module for running MUMmer and reading the output 3.044
assembly_improvement Improve the quality of a denovo assembly by scaffolding and gap filling 3.005
phandango an interactive viewer for populations of bacterial genomes linked by a phylogeny 2.972
companion Pipeline for automatic eukaryotic parasite annotation 2.944
assembly-stats Get assembly statistics from FASTA and FASTQ files 2.892
Bio-Tradis A set of tools to analyse the output from TraDIS analyses 2.881
Fastaq Python3 scripts to manipulate FASTA and FASTQ files 2.81
GeneDB Web front-end for genomic data, developed at the Pathogen Genomics group, Wellcome Trust Sanger Institute 2.81
panito Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment 2.74
plasmidtron Using kmers to find plasmids 2.654
mlst_check Multilocus sequence typing by blast using the schemes from PubMLST 2.612
saffrontree SaffronTree: Reference free rapid phylogenetic tree construction from raw read data 2.508
update_pipeline None 2.361
seroba None 2.303
pathogens-vm To build a virtual machine with some Sanger pathogens software installed 2.215
jobTree Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor) 2.068
progressiveCactus Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules 2.031
chado-export Script for exporting organism sequences from a CHADO database to GFF file. 1.997
sanger-pathogens.github.io Summary of Sanger Pathogen's Repos 1.976
MIDAS Front end for the HICF pathogen genome store 1.959
Web-Artemis None 1.883
citation_reporter Website to show your team's publications (which are in PubMed) 1.843
SnpEffWrapper Takes a VCF and applies annotations from a GFF using SnpEff 1.693
json2email Takes a jinja2 template and some json and sends an email 1.585
Bio-Metadata-Validator Validate a genome metadata manifest against a checklist 1.229
pathogen-informatics-training None 1.2
ariba-publication Supplementary data and scripts for ARIBA publication 1.099
ntd_website WTSI NTD website 1.03
Bio-Sequencescape-Schema DBIC schema for the sequencescape warehouse database 1.016
Bio-Track-Schema DBIC schema for pathogens tracking databases 1.011
Bio-PacbioMethylation Runs Pacbio methylation pipeline 1.009
companion-publication Accompanying information for the Companion publication 1.008
PySnpSites Experiments optimising python (with Cython) 1.008
ABACAS2 ABACAS2, a tool for ordering and orientating biosequences along a reference 1.007
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 0.603
Bio-HICF-Schema None 0.471
deago None 0.407
vr-codebase The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute 0.373
Farmpy Python3 package to handle job submission to a compute farm 0.304
crawl2 A spiritual successor to Crawl 0.276
Bio-RNASeq The new Sanger Pathogen Informatics RNA Seq analysis pipeline 0.221
annot-web Web interface for Companion 0.201
kraken Kraken taxonomic sequence classification system 0.2
fastml Addtional functionality for fastml, see http://fastml.tau.ac.il 0.2
deployment None 0.194
pipelines_reporting None 0.192
Farm_blast Python3 module to run blast+ or blastall in parallel on an LSF compute farm 0.161
Bio-Path-Find None 0.157
PathPipeConfTools Outputs details of all of the pathogen jobs in the pipeline 0.155
setup_tracking setup a vrtracking pipeline 0.137
reference_track None 0.137
find_files_for_deletion None 0.137
iva-publication Supplementary scripts and data for the IVA publication 0.101
Bio-AutomatedAnnotation Perl module to take in an genomic assembly and produce annoation 0.1
Bio-ENA-DataSubmission None 0.038
Bio-ReferenceManager None 0.035
remove_blocks_from_aln None 0.033
Bio-InterProScanWrapper None 0.027
Bio-VertRes-Config None 0.019
Bio-Metagenomics None 0.009
madansi None 0.008
orderedPainting None 0.0
Bio-VertRes-Permissions None 0.0
HICF_checklist None 0.0

Data collected: 2017-11-23T20:07:37Z