Featured Repos

Other Repos

Repository Description Score
gubbins Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins 47.581
circlator A tool to circularize genome assemblies 45.199
iva de novo virus assembler of Illumina paired reads 44.733
Bio-Tradis A set of tools to analyse the output from TraDIS analyses 4.034
plasmidtron Assembling the cause of phenotypes and genotypes from NGS data 3.835
snp-sites Finds SNP sites from a multi-FASTA alignment file 3.812
gff3toembl Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI 3.661
Fastaq Python3 scripts to manipulate FASTA and FASTQ files 3.567
mlst_check Multilocus sequence typing by blast using the schemes from PubMLST 3.15
companion Pipeline for automatic eukaryotic parasite annotation 3.148
saffrontree SaffronTree: Reference free rapid phylogenetic tree construction from raw read data 3.064
panito Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment 3.054
assembly_improvement Improve the quality of a denovo assembly by scaffolding and gap filling 3.024
pymummer Python3 module for running MUMmer and reading the output 2.898
ntd_website Wellcome Sanger Institute NTD website 2.506
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 2.397
AdminLTE AdminLTE - Free Premium Admin control Panel Theme Based On Bootstrap 3.x 2.318
krocus Predict MLST directly from uncorrected long reads 2.149
MIDAS Front end for the HICF pathogen genome store 2.135
SnpEffWrapper Takes a VCF and applies annotations from a GFF using SnpEff 2.055
update_pipeline None 2.013
phandango an interactive viewer for populations of bacterial genomes linked by a phylogeny 2.006
pathogen-informatics-training None 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
sanger-pathogens.github.io Summary of Sanger Pathogen's Repos 1.975
GeneDB-static Static version of GeneDB website 1.83
json2email Takes a jinja2 template and some json and sends an email 1.576
citation_reporter Website to show your team's publications (which are in PubMed) 1.373
Bio-Metadata-Validator Validate a genome metadata manifest against a checklist 1.206
GithubConglomerate Brings together details of github repos across organisations 1.176
chado-export Script for exporting organism sequences from a CHADO database to GFF file. 1.007
ariba-publication Supplementary data and scripts for ARIBA publication 1.001
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
deago None 0.864
seroba None 0.848
Bio-Deago None 0.337
vr-codebase The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute 0.329
crawl2 A spiritual successor to Crawl 0.298
Farmpy Python3 package to handle job submission to a compute farm 0.281
Bio-Metagenomics None 0.263
Bio-RNASeq The new Sanger Pathogen Informatics RNA Seq analysis pipeline 0.256
deployment None 0.256
Bio-ReferenceManager None 0.249
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
find_files_for_deletion None 0.181
pipelines_reporting None 0.181
setup_tracking setup a vrtracking pipeline 0.163
reference_track None 0.137
Bio-AutomatedAnnotation Perl module to take in an genomic assembly and produce annoation 0.126
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-Path-Find None 0.1
iva-publication Supplementary scripts and data for the IVA publication 0.1
Bio-InterProScanWrapper None 0.04
Bio-ENA-DataSubmission None 0.023
Bio-VertRes-Config None 0.003
Bio-HICF-Schema None 0.003
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: 2018-06-18T19:07:39Z