Featured Repos

Other Repos

Repository Description Score
iva de novo virus assembler of Illumina paired reads 48.12
ariba Antimicrobial Resistance Identification By Assembly 44.905
circlator A tool to circularize genome assemblies 42.456
gff3toembl Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI 3.821
snp-sites Finds SNP sites from a multi-FASTA alignment file 3.723
pymummer Python3 module for running MUMmer and reading the output 3.323
assembly_improvement Improve the quality of a denovo assembly by scaffolding and gap filling 3.019
companion Pipeline for automatic eukaryotic parasite annotation 2.938
plasmidtron Using kmers to find plasmids 2.908
Bio-Tradis A set of tools to analyse the output from TraDIS analyses 2.897
Fastaq Python3 scripts to manipulate FASTA and FASTQ files 2.824
GeneDB Web front-end for genomic data, developed at the Pathogen Genomics group, Wellcome Trust Sanger Institute 2.821
panito Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment 2.788
mlst_check Multilocus sequence typing by blast using the schemes from PubMLST 2.521
saffrontree SaffronTree: Reference free rapid phylogenetic tree construction from raw read data 2.519
primer3tools Design PCR primers and check uniqueness across multiple genomes 2.248
pathogens-vm To build a virtual machine with some Sanger pathogens software installed 2.228
BioPericles A work in progress. BioPericles is designed to use supervised Machine Learning techniques to classify samples into clusters 2.225
assembly-stats Get assembly statistics from FASTA and FASTQ files 2.201
jobTree Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor) 2.167
progressiveCactus Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules 2.075
bio_assembly_refinement Tools to refine/finish an assembly 2.074
Bio-DBAnnotationRemapper Relocate annotation in a database based on flat files (embl) 2.018
phandango an interactive viewer for populations of bacterial genomes linked by a phylogeny 2.005
degust A web tool for visualising differential gene expression data 2.0
sanger-pathogens.github.io Summary of Sanger Pathogen's Repos 1.975
MIDAS Front end for the HICF pathogen genome store 1.971
Web-Artemis None 1.894
pathogen-informatics-training None 1.86
update_pipeline None 1.844
SnpEffWrapper Takes a VCF and applies annotations from a GFF using SnpEff 1.704
json2email Takes a jinja2 template and some json and sends an email 1.598
citation_reporter Website to show your team's publications (which are in PubMed) 1.434
Assembly_tools Scripts relating to genome assemblies 1.389
annotation_store None 1.37
Bio-Metadata-Validator Validate a genome metadata manifest against a checklist 1.261
ntd_website WTSI NTD website 1.073
Bio-Sequencescape-Schema DBIC schema for the sequencescape warehouse database 1.039
Bio-Track-Schema DBIC schema for pathogens tracking databases 1.027
tracer TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data 1.023
eupathtables Python interface for reading and converting EuPathDB flat file dumps 1.021
Bio-PacbioMethylation Runs Pacbio methylation pipeline 1.021
companion-publication Accompanying information for the Companion publication 1.019
PySnpSites Experiments optimising python (with Cython) 1.019
ABACAS2 ABACAS2, a tool for ordering and orientating biosequences along a reference 1.018
DataPages Static pages with convenient links to WTSI's pathogen sequencing data 1.018
VarGeneAnalysis Code associated with some VarGene Analysis 1.018
pequeno Novel sequences 1.002
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
Bio-Deago None 0.994
Bio-RetrieveAssemblies None 0.75
seroba None 0.556
vr-codebase The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute 0.378
Farmpy Python3 package to handle job submission to a compute farm 0.367
crawl2 A spiritual successor to Crawl 0.277
crawl Chado Restful Access Webservice Layer 0.25
deployment None 0.231
Bio-Metagenomics None 0.228
resistome-db None 0.226
QUASR None 0.225
Bio-RNASeq The new Sanger Pathogen Informatics RNA Seq analysis pipeline 0.223
Farm_blast Python3 module to run blast+ or blastall in parallel on an LSF compute farm 0.22
PathPipeConfTools Outputs details of all of the pathogen jobs in the pipeline 0.204
annot-web Web interface for Companion 0.202
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 0.147
pipelines_reporting None 0.139
vrtrack_crawl None 0.139
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
validate_tools File validation scripts and tools 0.123
iva-publication Supplementary scripts and data for the IVA publication 0.102
PathFind Modularised versions of *find scripts 0.102
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-ReferenceManager None 0.085
remove_blocks_from_aln None 0.082
Bio-ENA-DataSubmission None 0.064
Bio-VertRes-Config None 0.047
bragv None 0.037
Bio-InterProScanWrapper None 0.036
ngs-ftp-uploader None 0.021
Bio-HICF-Schema None 0.021
artemis_runners None 0.019
Bio-Resistome None 0.019
trait_assembler None 0.019
madansi None 0.019
LSF_jobrunner_Roary None 0.002
Bio-GFFValidator None 0.002
Bio-TypingGenerator None 0.002
orderedPainting None 0.001
Bio-VertRes-Permissions None 0.0
HICF_checklist None 0.0
concordance None 0.0
annotations_update None 0.0
Bio-Pipeline-Comparison None 0.0

Data collected: 2017-10-18T19:07:53Z