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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 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
  • 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
  • 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
  • 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
  • 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
  • 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 0 0 Updated Mar 19, 2025
  • raredisease Public

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

    nf-core/raredisease’s past year of commit activity
    Nextflow 97 MIT 43 36 4 Updated Mar 19, 2025
  • deepmodeloptim Public

    Stochastic Testing and Input Manipulation for Unbiased Learning Systems

    nf-core/deepmodeloptim’s past year of commit activity
    Nextflow 26 MIT 12 22 (1 issue needs help) 0 Updated Mar 19, 2025
  • coproid Public

    Coprolite host Identification pipeline

    nf-core/coproid’s past year of commit activity
    Nextflow 9 MIT 4 2 0 Updated Mar 19, 2025
  • meerpipe Public

    nf-core/meerpipe is a astronomy pipeline that processes MeerKAT pulsar data to produce images and data products for pulsar timing analysis

    nf-core/meerpipe’s past year of commit activity
    Nextflow 7 MIT 5 2 1 Updated Mar 19, 2025
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