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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 237 188

  2. modules modules Public

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

    Nextflow 279 695

  3. rnaseq rnaseq Public

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

    Nextflow 884 702

  4. sarek sarek Public

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

    Nextflow 399 404

  5. chipseq chipseq Public

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

    Nextflow 190 145

  6. eager eager Public

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

    Nextflow 144 82

Repositories

Showing 10 of 138 repositories
  • proteinfold Public

    Protein 3D structure prediction pipeline

    nf-core/proteinfold’s past year of commit activity
    Nextflow 53 MIT 36 10 1 Updated Oct 17, 2024
  • detaxizer Public

    A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxa to identify (and remove) are Homo and Homo sapiens. Removal is optional.

    nf-core/detaxizer’s past year of commit activity
    Nextflow 13 MIT 5 1 0 Updated Oct 17, 2024
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    Astro 67 MIT 190 89 38 Updated Oct 17, 2024
  • rnafusion Public

    RNA-seq analysis pipeline for detection of gene-fusions

    nf-core/rnafusion’s past year of commit activity
    Nextflow 138 MIT 93 14 4 Updated Oct 17, 2024
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag’s past year of commit activity
    Nextflow 211 MIT 109 60 (1 issue needs help) 9 Updated Oct 17, 2024
  • test-datasets Public

    Test data to be used for automated testing with the nf-core pipelines

    nf-core/test-datasets’s past year of commit activity
    103 MIT 341 31 12 Updated Oct 17, 2024
  • raredisease Public

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

    nf-core/raredisease’s past year of commit activity
    Nextflow 85 MIT 34 35 1 Updated Oct 17, 2024
  • viralrecon Public

    Assembly and intrahost/low-frequency variant calling for viral samples

    nf-core/viralrecon’s past year of commit activity
    Nextflow 121 MIT 108 31 3 Updated Oct 17, 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 33 MIT 9 17 1 Updated Oct 17, 2024
  • createtaxdb Public

    Parallelised and automated construction of metagenomic classifier databases of different tools

    nf-core/createtaxdb’s past year of commit activity
    Nextflow 7 MIT 4 18 2 Updated Oct 17, 2024
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