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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 217 182

  2. modules modules Public

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

    Nextflow 258 653

  3. rnaseq rnaseq Public

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

    Nextflow 809 674

  4. sarek sarek Public

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

    Nextflow 350 387

  5. chipseq chipseq Public

    ChIP-seq peak-calling, QC and differential analysis pipeline.

    Nextflow 177 144

  6. eager eager Public

    A fully reproducible and state-of-the-art ancient DNA analysis pipeline

    Nextflow 128 78

Repositories

Showing 10 of 131 repositories
  • rnaseq Public

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

    nf-core/rnaseq’s past year of commit activity
    Nextflow 809 MIT 674 44 13 Updated Jul 4, 2024
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 258 MIT 653 395 (1 issue needs help) 117 Updated Jul 4, 2024
  • scdownstream Public

    A single cell transcriptomics pipeline for QC, integration and making the data presentable

    nf-core/scdownstream’s past year of commit activity
    Nextflow 5 MIT 3 17 2 Updated Jul 4, 2024
  • funcscan Public

    (Meta-)genome screening for functional and natural product gene sequences

    nf-core/funcscan’s past year of commit activity
    Nextflow 61 MIT 20 15 2 Updated Jul 4, 2024
  • variantbenchmarking Public

    A nextflow variant benchmarking pipeline - premature

    nf-core/variantbenchmarking’s past year of commit activity
    Nextflow 5 MIT 6 11 2 Updated Jul 4, 2024
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    Astro 64 MIT 181 83 34 Updated Jul 4, 2024
  • sarek Public

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

    nf-core/sarek’s past year of commit activity
    Nextflow 350 MIT 387 232 (3 issues need help) 25 Updated Jul 4, 2024
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag’s past year of commit activity
    Nextflow 191 MIT 102 48 (1 issue needs help) 4 Updated Jul 4, 2024
  • pangenome Public

    Renders a collection of sequences into a pangenome graph.

    nf-core/pangenome’s past year of commit activity
    Nextflow 56 MIT 15 10 1 Updated Jul 4, 2024
  • crisprseq Public

    A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).

    nf-core/crisprseq’s past year of commit activity
    Nextflow 21 MIT 23 19 2 Updated Jul 4, 2024
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