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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 324 189

  2. snp-sites snp-sites Public

    Finds SNP sites from a multi-FASTA alignment file

    C 241 50

  3. 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 239 77

  4. circlator circlator Public

    A tool to circularize genome assemblies

    Python 233 60

  5. ariba ariba Public

    Antimicrobial Resistance Identification By Assembly

    Python 172 55

  6. assembly-stats assembly-stats Public

    Get assembly statistics from FASTA and FASTQ files

    C++ 115 23

Repositories

Showing 10 of 92 repositories
  • Unicycler Public Forked from rrwick/Unicycler

    hybrid assembly pipeline for bacterial genomes

    sanger-pathogens/Unicycler’s past year of commit activity
    C++ 0 GPL-3.0 135 0 1 Updated Dec 3, 2024
  • assorted-sub-workflows Public
    sanger-pathogens/assorted-sub-workflows’s past year of commit activity
    Nextflow 0 AGPL-3.0 0 0 0 Updated Dec 3, 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 2 Updated Nov 28, 2024
  • generate_mags Public
    sanger-pathogens/generate_mags’s past year of commit activity
    Nextflow 1 0 0 0 Updated Nov 27, 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 Nov 19, 2024
  • Fastaq Public

    Python3 scripts to manipulate FASTA and FASTQ files

    sanger-pathogens/Fastaq’s past year of commit activity
    Python 70 21 8 2 Updated Nov 12, 2024
  • pymummer Public

    Python3 module for running MUMmer and reading the output

    sanger-pathogens/pymummer’s past year of commit activity
    Python 29 11 3 0 Updated Nov 12, 2024
  • bentley-app Public

    Static site for Stephen Bentley's group

    sanger-pathogens/bentley-app’s past year of commit activity
    JavaScript 0 0 0 1 Updated Nov 6, 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
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