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@cancerit

CASM IT

CASM IT provide bioinformatic support for Cancer, Ageing and Somatic Mutation group at the Wellcome Sanger Institute

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  1. ascatNgs Public

    Somatic copy number analysis using WGS paired end wholegenome sequencing

    Perl 69 17

  2. BRASS Public

    Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.

    Perl 57 20

  3. cgpPindel Public

    Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel

    Perl 28 5

  4. cgpCaVEManWrapper Public

    Reference implementation of CGP workflow for CaVEMan SNV analysis

    Perl 6 3

  5. proportionalmultibw Public

    JBrowse plugin to display multiple BigWig tracks as a stacked proportion

    JavaScript 3 1

  6. VAGrENT Public

    A toolset for comparing genomic variants to reference genome annotation to identify potential biological consequences

    Perl 8 7

Repositories

Showing 10 of 94 repositories
  • jbrowse-registry Public Forked from GMOD/jbrowse-registry

    JBrowse Plugin Registry

    HTML 0 BSD-2-Clause 8 0 9 Updated Jan 16, 2025
  • NanoSeq Public

    Analysis software for Nanorate Sequencing (NanoSeq) experiments

    C++ 15 AGPL-3.0 10 12 4 Updated Jan 15, 2025
  • LUCA Public

    Locus-based Universal CRISPR Aligner

    Python 0 GPL-3.0 0 0 0 Updated Dec 13, 2024
  • vafCorrect Public

    Calculates the Variant Allele Fraction of variants in VCF files

    Perl 19 AGPL-3.0 3 6 0 Updated Nov 28, 2024
  • QUANTS Public
    Python 1 MIT 3 3 1 Updated Nov 28, 2024
  • cgp-methpipe Public

    CGP implementation of Nextflow methylseq

    Shell 0 1 1 0 Updated Nov 18, 2024
  • cgpCaVEManWrapper Public

    Reference implementation of CGP workflow for CaVEMan SNV analysis

    Perl 6 AGPL-3.0 3 7 0 Updated Nov 15, 2024
  • hairpin2 Public

    artefact flagging algorithm based on Ellis et al. 2020 (DOI: 10.1038/s41596-020-00437-6) for LCM sequencing

    Python 0 0 1 0 Updated Nov 5, 2024
  • Python 0 MIT 2 1 0 Updated Oct 30, 2024
  • CaVEMan Public

    SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib

    C 60 AGPL-3.0 13 18 1 Updated Oct 25, 2024