Featured Repos

Other Repos

Repository Description Score
ariba Antimicrobial Resistance Identification By Assembly 41.516
gubbins Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins 41.313
circlator A tool to circularize genome assemblies 41.145
snp-sites Finds SNP sites from a multi-FASTA alignment file 4.322
update_pipeline Update a pipelines metadata 4.144
Bio-Tradis A set of tools to analyse the output from TraDIS analyses 3.91
chado-export A Python application for exporting organism sequences from a CHADO database to GFF file. 3.824
gff3toembl Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI 3.675
plasmidtron Assembling the cause of phenotypes and genotypes from NGS data 3.66
sanger-pathogens.github.io Summary of Sanger Pathogen's Repos 3.66
seroba k-mer based Pipeline to identify the Serotype from Illumina NGS reads 3.647
saffrontree SaffronTree: Reference free rapid phylogenetic tree construction from raw read data 3.46
pathogens-vm To build a virtual machine with some Sanger pathogens software installed 3.37
Fastaq Python3 scripts to manipulate FASTA and FASTQ files 3.345
json2email Takes a jinja2 template and some json and sends an email 3.268
chado-tools Tools for accessing CHADO databases. 3.222
archive_project Creating a backup to S3 of the pipeline results on nfs that aren't currently backed up. 3.185
mlst_check Multilocus sequence typing by blast using the schemes from PubMLST 3.175
panito Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment 3.128
assembly-stats Get assembly statistics from FASTA and FASTQ files 3.01
assembly_improvement Improve the quality of a denovo assembly by scaffolding and gap filling 3.0
bentley-app Static site for Stephen Bentley's group 2.991
companion Pipeline for automatic eukaryotic parasite annotation 2.984
juno-app Static site for the Juno project 2.969
pymummer Python3 module for running MUMmer and reading the output 2.965
docker-basher A set of bash functions to help create docker images 2.907
rnaseq Pathogen informatics RNA seq pipeline 2.726
gffmunger Munges GFF3 files exported from Chado (http://www.gmod.org/) database to make them suitable for loading into WebApollo. 2.702
external-import Import external data into our tracking databases 2.595
ntd_website Wellcome Sanger Institute NTD website 2.5
krocus Predict MLST directly from uncorrected long reads 2.37
java_launchers Scripts to launch java applications 2.327
manifest-validator A tool for validating the contents of a manifest before it enters pipelines 2.287
writedb_entry_set Repo to hold the writedb_entry_set Python code extracted from the Pathogen Informatics general GitLab repo. 2.208
SnpEffWrapper Takes a VCF and applies annotations from a GFF using SnpEff 2.185
GeneDB-static Static version of GeneDB website 2.128
eggnog-mapper Fast genome-wide functional annotation through orthology assignment 2.0
deago R package for generating HTML reports from differential expression analyis and GO term enrichment 2.0
bioconda-recipes Conda recipes for the bioconda channel. 2.0
AdminLTE AdminLTE - Free Premium Admin control Panel Theme Based On Bootstrap 3.x 2.0
phandango an interactive viewer for populations of bacterial genomes linked by a phylogeny 2.0
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
baker A tool to generate configuration files and wrapper scripts 1.98
bactgen-training-app Training site for the Juno/GPS2 projects 1.968
MIDAS Front end for the HICF pathogen genome store 1.95
fastqcheck Generate statistics on and validate fastq files 1.872
pathogen-informatics-training None 1.802
SPN-Resistance_Sanger Resistance pipeline for Sanger Cluster 1.694
software-tracker API and helper scripts for the pathogen software installation tracking database 1.509
structure Copy of Structure 2.3.4 with patch applied to fix seg fault 1.5
Bio-PacbioMethylation Runs Pacbio methylation pipeline 1.452
citation_reporter Website to show your team's publications (which are in PubMed) 1.37
gff_diff A tool to generate a JSON diff between two GFF files, written in Rust 1.214
Bio-Track-Schema DBIC schema for pathogens tracking databases 1.206
Bio-Metadata-Validator Validate a genome metadata manifest against a checklist 1.206
sapp Studies and Analysis in Pathogen Pipelines, a QCgrind rewrite 1.102
genedbot None 1.07
ABACAS2 ABACAS2, a tool for ordering and orientating biosequences along a reference 1.001
WebApollo-EbrcTracks fork of the EbrcTracks svn repository 1.0
conda-recipes Conda recipes for the sanger-pathogens channel: https://anaconda.org/sanger-pathogens 1.0
companion-publication Accompanying information for the Companion publication 1.0
GithubConglomerate Brings together details of github repos across organisations 1.0
Bio-Sequencescape-Schema DBIC schema for the sequencescape warehouse database 1.0
ariba-publication Supplementary data and scripts for ARIBA publication 1.0
PySnpSites Experiments optimising python (with Cython) 1.0
FMAP Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies 1.0
phandangoExampleData The data underlying the examples on https://jameshadfield.github.io/phandango 1.0
Bio-Metagenomics None 0.706
vr-codebase The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute 0.553
Farmpy Python3 package to handle job submission to a compute farm 0.335
PathPipeConfTools Outputs details of all of the pathogen jobs in the pipeline 0.297
Farm_blast Python3 module to run blast+ or blastall in parallel on an LSF compute farm 0.295
crawl2 A spiritual successor to Crawl 0.28
Bio-RNASeq The new Sanger Pathogen Informatics RNA Seq analysis pipeline 0.26
fastml Addtional functionality for fastml, see http://fastml.tau.ac.il 0.221
farm_rfam None 0.207
Bio-ReferenceManager None 0.206
annot-web Web interface for Companion 0.2
kraken Kraken taxonomic sequence classification system 0.2
deployment None 0.182
setup_tracking setup a vrtracking pipeline 0.158
Bio-AutomatedAnnotation Perl module to take in an genomic assembly and produce annoation 0.137
find_files_for_deletion None 0.137
reference_track None 0.137
Bio-Path-Find None 0.126
iva-publication Supplementary scripts and data for the IVA publication 0.121
Bio-VertRes-Config None 0.099
remove_blocks_from_aln None 0.089
Bio-ENA-DataSubmission None 0.071
Bio-InterProScanWrapper None 0.054
Bio-Deago None 0.0
Bio-HICF-Schema None 0.0
Bio-VertRes-Permissions None 0.0
madansi None 0.0
orderedPainting None 0.0
HICF_checklist None 0.0

Data collected: 2020-04-30T19:07:42Z