Featured Repos

Other Repos

Repository Description Score
circlator A tool to circularize genome assemblies 49.663
iva de novo virus assembler of Illumina paired reads 48.871
gubbins Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins 39.548
Bio-Tradis A set of tools to analyse the output from TraDIS analyses 4.109
Fastaq Python3 scripts to manipulate FASTA and FASTQ files 4.058
plasmidtron Assembling the cause of phenotypes and genotypes from NGS data 3.991
snp-sites Finds SNP sites from a multi-FASTA alignment file 3.865
gff3toembl Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI 3.661
companion Pipeline for automatic eukaryotic parasite annotation 3.302
panito Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment 3.193
saffrontree SaffronTree: Reference free rapid phylogenetic tree construction from raw read data 3.178
assembly_improvement Improve the quality of a denovo assembly by scaffolding and gap filling 3.046
pymummer Python3 module for running MUMmer and reading the output 2.899
mlst_check Multilocus sequence typing by blast using the schemes from PubMLST 2.641
ntd_website Wellcome Sanger Institute NTD website 2.622
AdminLTE AdminLTE - Free Premium Admin control Panel Theme Based On Bootstrap 3.x 2.59
assembly-stats Get assembly statistics from FASTA and FASTQ files 2.418
pathogens-vm To build a virtual machine with some Sanger pathogens software installed 2.37
MIDAS Front end for the HICF pathogen genome store 2.293
krocus Predict MLST directly from uncorrected long reads 2.276
update_pipeline None 2.062
phandango an interactive viewer for populations of bacterial genomes linked by a phylogeny 2.011
jobTree Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor) 2.001
progressiveCactus Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules 2.0
SnpEffWrapper Takes a VCF and applies annotations from a GFF using SnpEff 1.988
sanger-pathogens.github.io Summary of Sanger Pathogen's Repos 1.975
pathogen-informatics-training None 1.731
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) 1.375
GithubConglomerate Brings together details of github repos across organisations 1.326
Bio-Metadata-Validator Validate a genome metadata manifest against a checklist 1.207
deago None 1.088
seroba None 1.081
chado-export Script for exporting organism sequences from a CHADO database to GFF file. 1.013
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
Bio-ReferenceManager None 0.462
vr-codebase The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute 0.347
Bio-Metagenomics None 0.312
crawl2 A spiritual successor to Crawl 0.308
Farmpy Python3 package to handle job submission to a compute farm 0.281
Bio-RNASeq The new Sanger Pathogen Informatics RNA Seq analysis pipeline 0.257
deployment None 0.25
Bio-Deago None 0.242
find_files_for_deletion None 0.219
pipelines_reporting None 0.218
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 0.168
reference_track None 0.137
Bio-AutomatedAnnotation Perl module to take in an genomic assembly and produce annoation 0.131
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 0.103
iva-publication Supplementary scripts and data for the IVA publication 0.1
Bio-InterProScanWrapper None 0.057
Bio-ENA-DataSubmission None 0.025
Bio-VertRes-Config None 0.006
Bio-HICF-Schema None 0.005
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: 2018-05-24T19:07:37Z