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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 Public

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

    Python 251 198

  2. modules Public

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

    Nextflow 297 755

  3. 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 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
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    Nextflow 62 MIT 16 23 2 Updated Mar 19, 2025
  • pathogensurveillance Public

    Surveillance of pathogens using population genomics and sequencing

    Nextflow 18 MIT 6 53 (2 issues need help) 1 Updated Mar 18, 2025
  • modules Public

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

    Nextflow 297 MIT 755 466 (1 issue needs help) 127 Updated Mar 19, 2025
  • website Public

    Code and files for the main nf-core website.

    MDX 73 MIT 238 92 33 Updated Mar 18, 2025
  • stats Public
    HTML 0 2 13 10 Updated Mar 18, 2025
  • scnanoseq Public

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

    Nextflow 25 MIT 9 2 0 Updated Mar 18, 2025
  • rnafusion Public

    RNA-seq analysis pipeline for detection of gene-fusions

    Nextflow 150 MIT 106 47 (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

    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

    Nextflow 74 MIT 44 63 (1 issue needs help) 5 Updated Mar 18, 2025
  • raredisease Public

    Call and score variants from WGS/WES of rare disease patients.

    Nextflow 97 MIT 43 36 3 Updated Mar 18, 2025
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