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@nf-core

nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.

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  1. tools tools Public

    Python package with helper tools for the nf-core community.

    Python 244 192

  2. modules modules Public

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

    Nextflow 287 734

  3. rnaseq rnaseq Public

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

    Nextflow 938 712

  4. sarek sarek Public

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

    Nextflow 411 417

  5. chipseq chipseq Public

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

    Nextflow 199 150

  6. eager eager Public

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

    Nextflow 152 82

Repositories

Showing 10 of 148 repositories
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 1 2 48 9 Updated Dec 14, 2024
  • epitopeprediction Public

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

    nf-core/epitopeprediction’s past year of commit activity
    Nextflow 42 MIT 22 15 2 Updated Dec 14, 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 44 MIT 12 25 (4 issues need help) 3 Updated Dec 14, 2024
  • methylseq Public

    Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

    nf-core/methylseq’s past year of commit activity
    Nextflow 143 MIT 145 26 (2 issues need help) 4 Updated Dec 14, 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
    109 MIT 360 31 12 Updated Dec 14, 2024
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag’s past year of commit activity
    Nextflow 218 MIT 111 64 (1 issue needs help) 9 Updated Dec 14, 2024
  • stats Public
    nf-core/stats’s past year of commit activity
    HTML 0 0 9 10 Updated Dec 14, 2024
  • pacvar Public

    Longread PacBio sequencing processing for WGS and PureTarget

    nf-core/pacvar’s past year of commit activity
    Nextflow 1 MIT 1 1 4 Updated Dec 14, 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 287 MIT 734 460 (1 issue needs help) 187 Updated Dec 13, 2024
  • ampliseq Public

    Amplicon sequencing analysis workflow using DADA2 and QIIME2

    nf-core/ampliseq’s past year of commit activity
    Nextflow 189 MIT 120 27 6 Updated Dec 13, 2024