Pathogen Informatics, Wellcome Sanger Institute

Repositories

• monocle

  🧐 Data exploration tool for the Juno project

  react graphql django docker-compose graphene cypress
  JavaScript GPL-3.0 0 0 0 1 Updated Jul 6, 2020

• Bio-ReferenceManager
  Perl GPL-3.0 2 1 0 0 Updated Jul 2, 2020

• external-import

  Import external data into our tracking databases
  Python GPL-3.0 0 0 0 0 Updated Jul 1, 2020

• bactgen-training-app

  Static site for training on the Juno/GPS2 projects
  HTML 0 0 0 0 Updated Jul 1, 2020

• archive_project

  Tool to back up the data produced by the Pathogen Informatics sequencing pipelines to an S3 server
  Python GPL-3.0 0 0 0 0 Updated Jun 23, 2020

• saffrontree

  SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

  bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline
  Python GPL-3.0 5 15 1 0 Updated Jun 11, 2020

• plasmidtron

  Assembling the cause of phenotypes and genotypes from NGS data

  bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline
  Python GPL-3.0 8 16 2 0 Updated Jun 11, 2020

• circlator

  A tool to circularize genome assemblies

  bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline
  Python GPL-3.0 35 106 41 1 Updated Jun 9, 2020

• iva

  de novo virus assembler of Illumina paired reads

  bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline
  Python GPL-3.0 15 33 9 3 Updated Jun 9, 2020

• snp-sites

  Finds SNP sites from a multi-FASTA alignment file

  bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline
  C 35 103 10 0 Updated Jun 9, 2020

• gubbins

  Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

  bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline
  C GPL-2.0 29 59 36 0 Updated Jun 9, 2020

• Roary

  Rapid large-scale prokaryote pan genome analysis

  bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline
  Perl GPL-3.0 116 149 94 2 Updated Jun 9, 2020

• GeneDB-static

  Static version of GeneDB website
  JavaScript GPL-3.0 3 0 0 2 Updated Jun 8, 2020

• software-tracker

  API and helper scripts for the pathogen software installation tracking database
  Python 0 0 0 0 Updated Jun 8, 2020

• bentley-app

  Static site for Stephen Bentley's group
  JavaScript 0 0 0 0 Updated Jun 8, 2020

• ariba

  Antimicrobial Resistance Identification By Assembly

  bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline
  Python GPL-3.0 38 87 20 0 Updated Jun 7, 2020

• Bio-VertRes-Config
  Perl GPL-3.0 9 0 0 0 Updated Jun 4, 2020

• Bio-ENA-DataSubmission
  Perl GPL-3.0 8 2 0 0 Updated Jun 2, 2020

• assembly_improvement

  Improve the quality of a denovo assembly by scaffolding and gap filling

  bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline
  Perl GPL-3.0 20 34 7 1 Updated Jun 1, 2020

• vr-codebase

  Forked from VertebrateResequencing/vr-codebase

  The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute
  Perl 33 11 0 0 Updated May 22, 2020

• Bio-AutomatedAnnotation

  Perl module to take in an genomic assembly and produce annoation
  Perl GPL-3.0 8 0 0 0 Updated May 18, 2020

• singularity-bsub

  Provides wrapper scripts for executing LSF commands within a Singularity container
  Shell GPL-3.0 0 0 0 0 Updated May 14, 2020

• Bio-Metagenomics
  Perl GPL-3.0 2 1 0 0 Updated May 14, 2020

• Bio-RNASeq

  The new Sanger Pathogen Informatics RNA Seq analysis pipeline
  Perl GPL-3.0 8 5 0 0 Updated May 14, 2020

• mlst_check

  Multilocus sequence typing by blast using the schemes from PubMLST

  bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline
  Perl GPL-3.0 14 11 3 0 Updated May 12, 2020

• juno-app

  Static site for the Juno project
  JavaScript 0 0 0 0 Updated May 6, 2020

• Bio-Path-Find
  Perl GPL-3.0 5 0 0 0 Updated May 5, 2020

• java_launchers

  Scripts to launch java applications
  Shell GPL-3.0 0 0 0 1 Updated May 1, 2020

• sanger-pathogens.github.io

  Summary of Sanger Pathogen's Repos
  Python 2 5 0 0 Updated Apr 30, 2020

• pipelines_reporting
  Perl GPL-3.0 0 1 0 0 Updated Apr 29, 2020