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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 252 198

  2. modules modules Public

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

    Nextflow 297 756

  3. rnaseq rnaseq Public

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

    Nextflow 995 737

  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 156 repositories
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 73 MIT 240 92 33 Updated Mar 19, 2025
  • fetchngs Public

    Pipeline to fetch metadata and raw FastQ files from public databases

    nf-core/fetchngs’s past year of commit activity
    Nextflow 171 MIT 79 27 11 Updated Mar 19, 2025
  • genomeassembler Public

    Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads

    nf-core/genomeassembler’s past year of commit activity
    Nextflow 19 MIT 13 3 0 Updated Mar 19, 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
  • lncpipe Public Forked from likelet/LncPipe

    UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets

    nf-core/lncpipe’s past year of commit activity
    Nextflow 34 MIT 45 9 2 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 755 472 (1 issue needs help) 130 Updated Mar 19, 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) 6 Updated Mar 19, 2025
  • proposals Public

    Where new proposals for nf-core pipelines and more can be made

    nf-core/proposals’s past year of commit activity
    0 MIT 0 1 0 Updated Mar 19, 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 26 MIT 12 15 1 Updated Mar 19, 2025
  • proteinfamilies Public

    Generation and update of protein families

    nf-core/proteinfamilies’s past year of commit activity
    Nextflow 9 MIT 1 0 1 Updated Mar 19, 2025
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