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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 277 218

  2. modules modules Public

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

    Nextflow 385 932

  3. rnaseq rnaseq Public

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

    Nextflow 1.1k 809

  4. sarek sarek Public

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

    Nextflow 500 488

  5. configs configs Public

    Config files used to define parameters specific to compute environments at different Institutions

    Nextflow 104 333

  6. proposals proposals Public

    Where new ideas for nf-core pipelines, special interest groups and more are proposed

    8 3

Repositories

Showing 10 of 172 repositories
  • genomeqc Public

    Compare the quality of multiple genomes, along with their annotations.

    nf-core/genomeqc’s past year of commit activity
    Nextflow 18 MIT 16 56 (2 issues need help) 3 Updated Nov 7, 2025
  • variantbenchmarking Public

    Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research

    nf-core/variantbenchmarking’s past year of commit activity
    Nextflow 36 MIT 19 22 1 Updated Nov 7, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 81 MIT 253 109 27 Updated Nov 7, 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 385 MIT 932 397 (1 issue needs help) 161 Updated Nov 7, 2025
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag’s past year of commit activity
    Nextflow 250 MIT 142 72 (1 issue needs help) 11 Updated Nov 7, 2025
  • atacseq Public

    ATAC-seq peak-calling and QC analysis pipeline

    nf-core/atacseq’s past year of commit activity
    Nextflow 213 MIT 128 45 3 Updated Nov 7, 2025
  • epitopeprediction Public

    A bioinformatics best-practice analysis pipeline for epitope prediction and annotation

    nf-core/epitopeprediction’s past year of commit activity
    Nextflow 48 MIT 29 11 2 Updated Nov 7, 2025
  • metapep Public

    From metagenomes to epitopes and beyond

    nf-core/metapep’s past year of commit activity
    Nextflow 12 MIT 10 14 4 Updated Nov 7, 2025
  • hgtseq Public

    A pipeline to investigate horizontal gene transfer from NGS data

    nf-core/hgtseq’s past year of commit activity
    Nextflow 26 MIT 7 1 1 Updated Nov 7, 2025
  • createtaxdb Public

    Parallelised and automated construction of metagenomic classifier databases of different tools

    nf-core/createtaxdb’s past year of commit activity
    Nextflow 15 MIT 10 11 1 Updated Nov 7, 2025
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