Featured Repos

Other Repos

Repository Description Score
gubbins Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins 51.514
circlator A tool to circularize genome assemblies 42.469
iva de novo virus assembler of Illumina paired reads 42.182
snp-sites Finds SNP sites from a multi-FASTA alignment file 4.644
plasmidtron Assembling the cause of phenotypes and genotypes from NGS data 4.61
gff3toembl Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI 4.535
Bio-Tradis A set of tools to analyse the output from TraDIS analyses 3.986
saffrontree SaffronTree: Reference free rapid phylogenetic tree construction from raw read data 3.848
mlst_check Multilocus sequence typing by blast using the schemes from PubMLST 3.55
ntd_website Wellcome Sanger Institute NTD website 3.541
Fastaq Python3 scripts to manipulate FASTA and FASTQ files 3.267
companion Pipeline for automatic eukaryotic parasite annotation 3.054
assembly_improvement Improve the quality of a denovo assembly by scaffolding and gap filling 3.01
panito Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment 2.969
pymummer Python3 module for running MUMmer and reading the output 2.897
pathogens-vm To build a virtual machine with some Sanger pathogens software installed 2.5
assembly-stats Get assembly statistics from FASTA and FASTQ files 2.383
krocus Predict MLST directly from uncorrected long reads 2.277
AdminLTE AdminLTE - Free Premium Admin control Panel Theme Based On Bootstrap 3.x 2.151
MIDAS Front end for the HICF pathogen genome store 2.038
phandango an interactive viewer for populations of bacterial genomes linked by a phylogeny 2.003
jobTree Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor) 2.0
progressiveCactus Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules 2.0
update_pipeline None 1.983
sanger-pathogens.github.io Summary of Sanger Pathogen's Repos 1.975
SnpEffWrapper Takes a VCF and applies annotations from a GFF using SnpEff 1.969
chado-export Script for exporting organism sequences from a CHADO database to GFF file. 1.737
pathogen-informatics-training None 1.716
json2email Takes a jinja2 template and some json and sends an email 1.576
deago None 1.54
GeneDB-static Static version of GeneDB website 1.52
seroba None 1.459
citation_reporter Website to show your team's publications (which are in PubMed) 1.371
Bio-Metadata-Validator Validate a genome metadata manifest against a checklist 1.206
GithubConglomerate Brings together details of github repos across organisations 1.084
ariba-publication Supplementary data and scripts for ARIBA publication 1.0
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-Deago None 0.873
vr-codebase The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute 0.318
crawl2 A spiritual successor to Crawl 0.289
Farmpy Python3 package to handle job submission to a compute farm 0.281
Bio-RNASeq The new Sanger Pathogen Informatics RNA Seq analysis pipeline 0.246
Bio-Metagenomics None 0.233
deployment None 0.229
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 0.16
find_files_for_deletion None 0.158
pipelines_reporting None 0.158
reference_track None 0.137
Bio-AutomatedAnnotation Perl module to take in an genomic assembly and produce annoation 0.123
Farm_blast Python3 module to run blast+ or blastall in parallel on an LSF compute farm 0.121
PathPipeConfTools Outputs details of all of the pathogen jobs in the pipeline 0.121
Bio-ReferenceManager None 0.118
iva-publication Supplementary scripts and data for the IVA publication 0.1
Bio-Path-Find None 0.099
Bio-InterProScanWrapper None 0.03
Bio-ENA-DataSubmission None 0.022
Bio-VertRes-Config None 0.002
Bio-HICF-Schema None 0.001
remove_blocks_from_aln None 0.0
madansi None 0.0
orderedPainting None 0.0
Bio-VertRes-Permissions None 0.0
HICF_checklist None 0.0

Data collected: 2018-07-18T19:07:48Z