Featured Repos

Other Repos

Repository Description Score
ariba Antimicrobial Resistance Identification By Assembly 48.915
circlator A tool to circularize genome assemblies 44.459
iva de novo virus assembler of Illumina paired reads 40.148
gff3toembl Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI 3.956
snp-sites Finds SNP sites from a multi-FASTA alignment file 3.754
pymummer Python3 module for running MUMmer and reading the output 3.707
plasmidtron Using kmers to find plasmids 3.257
assembly_improvement Improve the quality of a denovo assembly by scaffolding and gap filling 3.041
companion Pipeline for automatic eukaryotic parasite annotation 2.93
Bio-Tradis A set of tools to analyse the output from TraDIS analyses 2.919
panito Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment 2.854
Fastaq Python3 scripts to manipulate FASTA and FASTQ files 2.843
GeneDB Web front-end for genomic data, developed at the Pathogen Genomics group, Wellcome Trust Sanger Institute 2.837
mlst_check Multilocus sequence typing by blast using the schemes from PubMLST 2.538
saffrontree SaffronTree: Reference free rapid phylogenetic tree construction from raw read data 2.534
jobTree Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor) 2.302
pathogens-vm To build a virtual machine with some Sanger pathogens software installed 2.245
BioPericles A work in progress. BioPericles is designed to use supervised Machine Learning techniques to classify samples into clusters 2.241
assembly-stats Get assembly statistics from FASTA and FASTQ files 2.192
progressiveCactus Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules 2.137
bio_assembly_refinement Tools to refine/finish an assembly 2.09
Bio-DBAnnotationRemapper Relocate annotation in a database based on flat files (embl) 2.032
phandango an interactive viewer for populations of bacterial genomes linked by a phylogeny 2.009
degust A web tool for visualising differential gene expression data 2.0
MIDAS Front end for the HICF pathogen genome store 1.988
sanger-pathogens.github.io Summary of Sanger Pathogen's Repos 1.975
Web-Artemis None 1.909
update_pipeline None 1.879
SnpEffWrapper Takes a VCF and applies annotations from a GFF using SnpEff 1.719
json2email Takes a jinja2 template and some json and sends an email 1.615
citation_reporter Website to show your team's publications (which are in PubMed) 1.486
primer3tools Design PCR primers and check uniqueness across multiple genomes 1.409
Assembly_tools Scripts relating to genome assemblies 1.405
annotation_store None 1.37
Bio-Metadata-Validator Validate a genome metadata manifest against a checklist 1.306
ntd_website WTSI NTD website 1.133
Bio-Sequencescape-Schema DBIC schema for the sequencescape warehouse database 1.07
Bio-Track-Schema DBIC schema for pathogens tracking databases 1.049
tracer TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data 1.042
eupathtables Python interface for reading and converting EuPathDB flat file dumps 1.039
Bio-PacbioMethylation Runs Pacbio methylation pipeline 1.039
companion-publication Accompanying information for the Companion publication 1.035
PySnpSites Experiments optimising python (with Cython) 1.034
ABACAS2 ABACAS2, a tool for ordering and orientating biosequences along a reference 1.032
DataPages Static pages with convenient links to WTSI's pathogen sequencing data 1.032
VarGeneAnalysis Code associated with some VarGene Analysis 1.032
pequeno Novel sequences 1.003
FMAP Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies 1.001
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
pathogen-informatics-training None 0.832
Bio-RetrieveAssemblies None 0.75
seroba None 0.633
vr-codebase The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute 0.374
Farmpy Python3 package to handle job submission to a compute farm 0.327
crawl2 A spiritual successor to Crawl 0.279
crawl Chado Restful Access Webservice Layer 0.25
Bio-Metagenomics None 0.245
resistome-db None 0.241
QUASR None 0.241
deployment None 0.234
Bio-RNASeq The new Sanger Pathogen Informatics RNA Seq analysis pipeline 0.224
annot-web Web interface for Companion 0.204
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 None 0.188
Bio-ReferenceManager None 0.154
pipelines_reporting None 0.141
vrtrack_crawl None 0.14
setup_tracking setup a vrtracking pipeline 0.137
reference_track None 0.137
find_files_for_deletion None 0.137
gap5_consistency_checker 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 0.125
validate_tools File validation scripts and tools 0.124
iva-publication Supplementary scripts and data for the IVA publication 0.104
PathFind Modularised versions of *find scripts 0.103
Bio-AutomatedAnnotation Perl module to take in an genomic assembly and produce annoation 0.1
fasta_grep Efficiently pull filter FASTA files 0.1
Bio-ENA-DataSubmission None 0.098
Bio-VertRes-Config None 0.085
Bio-InterProScanWrapper None 0.048
ngs-ftp-uploader None 0.039
Bio-HICF-Schema None 0.038
bragv None 0.037
artemis_runners None 0.035
Bio-Resistome None 0.034
trait_assembler None 0.034
madansi None 0.034
LSF_jobrunner_Roary None 0.004
Bio-GFFValidator None 0.003
Bio-TypingGenerator None 0.003
orderedPainting None 0.001
Bio-VertRes-Permissions None 0.0
HICF_checklist None 0.0
concordance None 0.0
remove_blocks_from_aln None 0.0
annotations_update None 0.0
Bio-Pipeline-Comparison None 0.0

Data collected: 2017-09-24T19:07:48Z