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@nf-core

nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.
README.md

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  1. tools tools Public

    Python package with helper tools for the nf-core community.

    Python 251 198

  2. modules modules Public

    Repository to host tool-specific module files for the Nextflow DSL2 community!

    Nextflow 297 755

  3. rnaseq rnaseq Public

    RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

    Nextflow 994 736

  4. sarek sarek Public

    Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

    Nextflow 431 434

Repositories

Showing 10 of 155 repositories
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 73 MIT 238 92 33 Updated Mar 19, 2025
  • test-datasets Public

    Test data to be used for automated testing with the nf-core pipelines

    nf-core/test-datasets’s past year of commit activity
    117 MIT 368 31 10 Updated Mar 19, 2025
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 62 MIT 16 23 2 Updated Mar 18, 2025
  • pathogensurveillance Public

    Surveillance of pathogens using population genomics and sequencing

    nf-core/pathogensurveillance’s past year of commit activity
    Nextflow 18 MIT 6 53 (2 issues need help) 1 Updated Mar 19, 2025
  • modules Public

    Repository to host tool-specific module files for the Nextflow DSL2 community!

    nf-core/modules’s past year of commit activity
    Nextflow 297 MIT 755 466 (1 issue needs help) 127 Updated Mar 18, 2025
  • stats Public
    nf-core/stats’s past year of commit activity
    HTML 0 2 13 10 Updated Mar 18, 2025
  • scnanoseq Public

    Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics

    nf-core/scnanoseq’s past year of commit activity
    Nextflow 25 MIT 9 2 0 Updated Mar 18, 2025
  • rnafusion Public

    RNA-seq analysis pipeline for detection of gene-fusions

    nf-core/rnafusion’s past year of commit activity
    Nextflow 150 MIT 106 46 (5 issues need help) 7 Updated Mar 18, 2025
  • references Public

    nf-core/references is a bioinformatics pipeline that build references, for multiple use cases

    nf-core/references’s past year of commit activity
    Nextflow 11 MIT 4 17 0 Updated Mar 18, 2025
  • differentialabundance Public

    Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

    nf-core/differentialabundance’s past year of commit activity
    Nextflow 74 MIT 44 63 (1 issue needs help) 5 Updated Mar 19, 2025
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