Featured Repos

Other Repos

Repository Description Score
ariba Antibiotic Resistance Identification By Assembly 47.74
iva de novo virus assembler of Illumina paired reads 45.828
gubbins Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins 42.813
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 4.545
Fastaq Python3 scripts to manipulate FASTA and FASTQ files 4.225
snp-sites Finds SNP sites from a multi-FASTA alignment file 3.799
companion Pipeline for automatic eukaryotic parasite annotation 3.489
assembly_improvement Improve the quality of a denovo assembly by scaffolding and gap filling 3.378
Bio-Tradis A set of tools to analyse the output from TraDIS analyses 3.205
GeneDB Web front-end for genomic data, developed at the Pathogen Genomics group, Wellcome Trust Sanger Institute 3.128
gff3toembl Converts PROKKA GFF3 files to EMBL files for uploading annotated assemblies to EBI 2.904
Bio-DBAnnotationRemapper Relocate annotation in a database based on flat files (embl) 2.429
pathogens-vm To build a virtual machine with some Sanger pathogens software installed 2.28
panito Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment 2.276
update_pipeline 2.23
BioPericles A work in progress. BioPericles is designed to use supervised Machine Learning techniques to classify samples into clusters 2.206
MIDAS Front end for the HICF pathogen genome store 2.05
bio_assembly_refinement Tools to refine/finish an assembly 1.975
sanger-pathogens.github.io Summary of Sanger Pathogen's Repos 1.975
Web-Artemis 1.901
assembly-stats Get assembly statistics from FASTA and FASTQ files 1.706
SnpEffWrapper Takes a VCF and applies annotations from a GFF using SnpEff 1.687
Bio-Metadata-Validator Validate a genome metadata manifest against a checklist 1.634
json2email Takes a jinja2 template and some json and sends an email 1.576
Bio-Sequencescape-Schema DBIC schema for the sequencescape warehouse database 1.428
Bio-Track-Schema DBIC schema for pathogens tracking databases 1.428
citation_reporter Website to show your team's publications (which are in PubMed) 1.377
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-RetrieveAssemblies 1.178
eupathtables Python interface for reading and converting EuPathDB flat file dumps 1.092
DataPages Static pages with convenient links to WTSI's pathogen sequencing data 1.009
VarGeneAnalysis Code associated with some VarGene Analysis 1.008
companion-publication Accompanying information for the Companion publication 1.008
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 0.929
Bio-Metagenomics 0.634
Bio-Resistome 0.428
vr-codebase The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute 0.363
crawl2 A spiritual successor to Crawl 0.28
Bio-RNASeq The new Sanger Pathogen Informatics RNA Seq analysis pipeline 0.263
deployment 0.262
crawl Chado Restful Access Webservice Layer 0.25
annot-web Web interface for Companion 0.236
Farmpy Python3 package to handle job submission to a compute farm 0.226
pathogen-informatics-training 0.209
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
Bio-Path-Find 0.18
vrtrack_crawl 0.18
setup_tracking setup a vrtracking pipeline 0.18
pipelines_reporting 0.18
PathFind Modularised versions of *find scripts 0.143
reference_track 0.137
find_files_for_deletion 0.137
gap5_consistency_checker 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 0.063
Bio-InterProScanWrapper 0.061
Bio-VertRes-Config 0.056
Bio-HICF-Schema 0.045
Bio-HPS-FastTrack 0.043
Bio-Pequeno 0.043
Bio-TypingGenerator 0.043
Bio-VertRes-Permissions 0.043
Bio-GFFValidator 0.043
bragv 0.037
trait_assembler 0.013
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: 2016-08-24T19:07:44Z