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@sanger-pathogens

Pathogen Informatics, Wellcome Sanger Institute

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  1. Roary Roary Public

    Rapid large-scale prokaryote pan genome analysis

    Perl 323 190

  2. Artemis Artemis Public

    Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

    Java 238 76

  3. snp-sites snp-sites Public

    Finds SNP sites from a multi-FASTA alignment file

    C 238 50

  4. circlator circlator Public

    A tool to circularize genome assemblies

    Python 232 59

  5. ariba ariba Public

    Antimicrobial Resistance Identification By Assembly

    Python 171 54

  6. assembly-stats assembly-stats Public

    Get assembly statistics from FASTA and FASTQ files

    C++ 115 23

Repositories

Showing 10 of 88 repositories
  • assorted-sub-workflows Public
    sanger-pathogens/assorted-sub-workflows’s past year of commit activity
    Nextflow 0 AGPL-3.0 0 0 0 Updated Oct 31, 2024
  • nextflow-commons Public

    Store of generic templates and scripts for nextflow pipelines

    sanger-pathogens/nextflow-commons’s past year of commit activity
    Nextflow 1 AGPL-3.0 0 0 3 Updated Sep 16, 2024
  • Multiple-mappings-to-bam Public

    A GSoC project - Nextflow pipeline updating the legacy Python2 Multiple mappings to bam to nextflow.

    sanger-pathogens/Multiple-mappings-to-bam’s past year of commit activity
    Python 2 0 0 0 Updated Aug 23, 2024
  • nano-rave Public

    Nextflow pipeline designed for rapid onsite QC and variant calling of Oxford Nanopore data (following basecalling and demultiplexing with Guppy).

    sanger-pathogens/nano-rave’s past year of commit activity
    Nextflow 11 AGPL-3.0 4 1 0 Updated Aug 9, 2024
  • TpRNAseq Public

    A bacterial RNAseq pipeline, designed for analysis of Treponema pallidum data

    sanger-pathogens/TpRNAseq’s past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Aug 8, 2024
  • nextflowtool Public
    sanger-pathogens/nextflowtool’s past year of commit activity
    Groovy 0 AGPL-3.0 0 0 0 Updated Jul 22, 2024
  • long-read-ampliseq Public
    sanger-pathogens/long-read-ampliseq’s past year of commit activity
    Nextflow 2 AGPL-3.0 0 0 0 Updated Jul 18, 2024
  • sh16_scripts Public archive

    Deprecated scripts for reference only

    sanger-pathogens/sh16_scripts’s past year of commit activity
    Python 0 0 0 0 Updated Jul 18, 2024
  • software-tracker Public

    API and helper scripts for the pathogen software installation tracking database

    sanger-pathogens/software-tracker’s past year of commit activity
    Python 0 MIT 1 1 0 Updated Jul 12, 2024
  • Artemis Public

    Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

    sanger-pathogens/Artemis’s past year of commit activity
    Java 238 76 29 4 Updated Jun 15, 2024
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