Featured Repos

Other Repos

Repository Description Score
circlator A tool to circularize genome assemblies 50.973
iva de novo virus assembler of Illumina paired reads 50.253
gubbins Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins 47.224
snp-sites Finds SNP sites from a multi-FASTA alignment file 4.796
Fastaq Python3 scripts to manipulate FASTA and FASTQ files 4.672
Bio-Tradis A set of tools to analyse the output from TraDIS analyses 3.675
gff3toembl Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI 3.661
assembly_improvement Improve the quality of a denovo assembly by scaffolding and gap filling 3.445
GeneDB Web front-end for genomic data, developed at the Pathogen Genomics group, Wellcome Trust Sanger Institute 3.376
plasmidtron Using kmers to find plasmids 3.258
ntd_website Wellcome Sanger Institute NTD website 3.055
saffrontree SaffronTree: Reference free rapid phylogenetic tree construction from raw read data 3.027
companion Pipeline for automatic eukaryotic parasite annotation 2.961
mlst_check Multilocus sequence typing by blast using the schemes from PubMLST 2.945
update_pipeline None 2.913
pymummer Python3 module for running MUMmer and reading the output 2.87
assembly-stats Get assembly statistics from FASTA and FASTQ files 2.837
panito Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment 2.813
pathogens-vm To build a virtual machine with some Sanger pathogens software installed 2.207
phandango an interactive viewer for populations of bacterial genomes linked by a phylogeny 2.097
jobTree Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor) 2.007
progressiveCactus Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules 2.003
sanger-pathogens.github.io Summary of Sanger Pathogen's Repos 1.976
MIDAS Front end for the HICF pathogen genome store 1.951
Web-Artemis None 1.876
SnpEffWrapper Takes a VCF and applies annotations from a GFF using SnpEff 1.686
json2email Takes a jinja2 template and some json and sends an email 1.577
pathogen-informatics-training None 1.554
citation_reporter Website to show your team's publications (which are in PubMed) 1.417
Bio-Metadata-Validator Validate a genome metadata manifest against a checklist 1.209
Bio-Metagenomics None 1.163
seroba None 1.144
chado-export Script for exporting organism sequences from a CHADO database to GFF file. 1.118
ariba-publication Supplementary data and scripts for ARIBA publication 1.01
Bio-Sequencescape-Schema DBIC schema for the sequencescape warehouse database 1.002
Bio-Track-Schema DBIC schema for pathogens tracking databases 1.001
Bio-PacbioMethylation Runs Pacbio methylation pipeline 1.001
companion-publication Accompanying information for the Companion publication 1.001
PySnpSites Experiments optimising python (with Cython) 1.001
ABACAS2 ABACAS2, a tool for ordering and orientating biosequences along a reference 1.001
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
GithubConglomerate Brings together details of github repos across organisations 1.0
structure Copy of Structure 2.3.4 with patch applied to fix seg fault 1.0
Bio-Deago None 0.438
vr-codebase The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute 0.407
crawl2 A spiritual successor to Crawl 0.275
Farmpy Python3 package to handle job submission to a compute farm 0.265
setup_tracking setup a vrtracking pipeline 0.253
Bio-RNASeq The new Sanger Pathogen Informatics RNA Seq analysis pipeline 0.221
Bio-AutomatedAnnotation Perl module to take in an genomic assembly and produce annoation 0.216
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
deployment None 0.188
Bio-Path-Find None 0.146
pipelines_reporting None 0.142
reference_track None 0.137
find_files_for_deletion None 0.137
Farm_blast Python3 module to run blast+ or blastall in parallel on an LSF compute farm 0.125
PathPipeConfTools Outputs details of all of the pathogen jobs in the pipeline 0.124
iva-publication Supplementary scripts and data for the IVA publication 0.1
Bio-ENA-DataSubmission None 0.058
Bio-VertRes-Config None 0.057
Bio-HICF-Schema None 0.047
deago None 0.041
Bio-InterProScanWrapper None 0.021
Bio-ReferenceManager None 0.003
remove_blocks_from_aln None 0.003
madansi None 0.001
orderedPainting None 0.0
Bio-VertRes-Permissions None 0.0
HICF_checklist None 0.0

Data collected: 2018-02-24T20:07:50Z