Featured Repos

Other Repos

Repository Description Score
ariba Antibiotic Resistance Identification By Assembly 45.057
iva de novo virus assembler of Illumina paired reads 44.953
gubbins Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins 41.383
rapid_annotation_transfer_tool RATT: A tool for transferring genomic annotations between genomes 10.0
pymummer Python3 module for running MUMmer and reading the output 4.278
Fastaq Python3 scripts to manipulate FASTA and FASTQ files 4.021
snp-sites Finds SNP sites from a multi-FASTA alignment file 3.781
GeneDB Web front-end for genomic data, developed at the Pathogen Genomics group, Wellcome Trust Sanger Institute 3.749
companion Pipeline for automatic eukaryotic parasite annotation 3.394
assembly_improvement Improve the quality of a denovo assembly by scaffolding and gap filling 3.329
Bio-Tradis A set of tools to analyse the output from TraDIS analyses 3.141
gff3toembl Converts PROKKA GFF3 files to EMBL files for uploading annotated assemblies to EBI 2.889
Bio-DBAnnotationRemapper Relocate annotation in a database based on flat files (embl) 2.37
pathogens-vm To build a virtual machine with some Sanger pathogens software installed 2.27
panito Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment 2.267
BioPericles A work in progress. BioPericles is designed to use supervised Machine Learning techniques to classify samples into clusters 2.206
update_pipeline 2.171
MIDAS Front end for the HICF pathogen genome store 2.036
assembly-stats Get assembly statistics from FASTA and FASTQ files 2.008
bio_assembly_refinement Tools to refine/finish an assembly 1.963
Web-Artemis 1.901
sanger-pathogens.github.io Summary of Sanger Pathogen's Repos 1.861
SnpEffWrapper Takes a VCF and applies annotations from a GFF using SnpEff 1.687
json2email Takes a jinja2 template and some json and sends an email 1.576
Bio-Metadata-Validator Validate a genome metadata manifest against a checklist 1.575
citation_reporter Website to show your team's publications (which are in PubMed) 1.376
primer3tools Design PCR primers and check uniqueness across multiple genomes 1.37
Assembly_tools Scripts relating to genome assemblies 1.37
annotation_store 1.37
Bio-Sequencescape-Schema DBIC schema for the sequencescape warehouse database 1.369
Bio-Track-Schema DBIC schema for pathogens tracking databases 1.369
Bio-RetrieveAssemblies 1.119
eupathtables Python interface for reading and converting EuPathDB flat file dumps 1.079
DataPages Static pages with convenient links to WTSI's pathogen sequencing data 1.007
VarGeneAnalysis Code associated with some VarGene Analysis 1.007
companion-publication Accompanying information for the Companion publication 1.007
ABACAS2 ABACAS2, a tool for ordering and orientating biosequences along a reference 1.0
PySnpSites Experiments optimising python (with Cython) 1.0
structure Copy of Structure 2.3.4 with patch applied to fix seg fault 1.0
mlst_check 0.87
Bio-Metagenomics 0.575
Bio-Resistome 0.369
vr-codebase The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute 0.352
crawl2 A spiritual successor to Crawl 0.28
Bio-RNASeq The new Sanger Pathogen Informatics RNA Seq analysis pipeline 0.258
deployment 0.25
crawl Chado Restful Access Webservice Layer 0.25
annot-web Web interface for Companion 0.231
Farmpy Python3 package to handle job submission to a compute farm 0.225
pathogen-informatics-training 0.208
QUASR 0.206
resistome-db 0.206
kraken Kraken taxonomic sequence classification system 0.2
fastml Addtional functionality for fastml, see http://fastml.tau.ac.il 0.2
vr-pipe Generic pipeline system 0.2
vrtrack_crawl 0.174
setup_tracking setup a vrtracking pipeline 0.174
pipelines_reporting 0.174
Bio-Path-Find 0.169
reference_track 0.137
find_files_for_deletion 0.137
gap5_consistency_checker 0.137
PathFind Modularised versions of *find scripts 0.137
PathPipeConfTools Outputs details of all of the pathogen jobs in the pipeline 0.121
Farm_blast Python3 module to run blast+ or blastall in parallel on an LSF compute farm 0.121
iva-publication Supplementary scripts and data for the IVA publication 0.121
validate_tools File validation scripts and tools 0.121
Bio-AutomatedAnnotation Perl module to take in an genomic assembly and produce annoation 0.102
fasta_grep Efficiently pull filter FASTA files 0.1
Bio-ENA-DataSubmission 0.058
Bio-InterProScanWrapper 0.056
Bio-VertRes-Config 0.048
Bio-HICF-Schema 0.039
bragv 0.037
Bio-HPS-FastTrack 0.037
Bio-Pequeno 0.037
Bio-TypingGenerator 0.037
Bio-VertRes-Permissions 0.037
Bio-GFFValidator 0.037
trait_assembler 0.011
HICF_checklist 0.001
concordance 0.0
LSF_jobrunner_Roary 0.0
remove_blocks_from_aln 0.0
annotations_update 0.0
Bio-Pipeline-Comparison 0.0

Data collected: 2016-08-30T19:07:43Z