@sanger-pathogens

Pathogen Genomics, Wellcome Trust Sanger Institute

  • Validate a genome metadata manifest against a checklist

    Perl 1 3 Updated Jun 23, 2017
  • Perl 1 Updated Jun 23, 2017
  • Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

    Shell 13 16 Updated Jun 21, 2017
  • Using kmers to find plasmids

    Python 6 4 Updated Jun 21, 2017
  • Rapid large-scale prokaryote pan genome analysis

    Perl 45 40 Updated Jun 21, 2017
  • Python 1 Updated Jun 20, 2017
  • The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute

    Perl 8 26 Updated Jun 19, 2017
  • Perl 7 13 Updated Jun 13, 2017
  • Perl 5 13 Updated Jun 12, 2017
  • Finds SNP sites from a multi-FASTA alignment file

    C 25 14 Updated Jun 9, 2017
  • DBIC schema for the sequencescape warehouse database

    Perl 2 Updated Jun 9, 2017
  • DBIC schema for pathogens tracking databases

    Perl 3 Updated May 25, 2017
  • Perl 5 Updated May 25, 2017
  • Improve the quality of a denovo assembly by scaffolding and gap filling

    Perl 21 15 Updated May 25, 2017
  • Perl 9 Updated May 25, 2017
  • A set of tools to analyse the output from TraDIS analyses

    Perl 3 16 Updated May 25, 2017
  • Python3 package to handle job submission to a compute farm

    Python 2 Updated May 25, 2017
  • Antimicrobial Resistance Identification By Assembly

    Python 19 9 Updated May 24, 2017
  • TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data

    Python 14 Updated May 19, 2017
  • To build a virtual machine with some Sanger pathogens software installed

    Shell 1 4 Updated May 16, 2017
  • Web interface for Companion

    Ruby 2 Updated May 16, 2017
  • Takes a jinja2 template and some json and sends an email

    Python 1 2 Updated May 16, 2017
  • Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

    Python 13 7 Updated May 16, 2017
  • de novo virus assembler of Illumina paired reads

    Python 16 7 Updated May 16, 2017
  • Python3 module for running MUMmer and reading the output

    Python 8 3 Updated May 16, 2017
  • Python3 scripts to manipulate FASTA and FASTQ files

    Python 7 7 Updated May 16, 2017
  • A tool to circularize genome assemblies

    Python 38 12 Updated May 16, 2017
  • Python 1 Updated May 16, 2017
  • Python interface for reading and converting EuPathDB flat file dumps

    Python 2 Updated May 16, 2017
  • Website to show your team's publications (which are in PubMed)

    Python 2 Updated May 16, 2017