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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 246 193

  2. modules modules Public

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

    Nextflow 291 749

  3. rnaseq rnaseq Public

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

    Nextflow 974 717

  4. sarek sarek Public

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

    Nextflow 421 424

  5. chipseq chipseq Public

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

    Nextflow 204 149

  6. eager eager Public

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

    Nextflow 158 82

Repositories

Showing 10 of 152 repositories
  • fastqrepair Public

    A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered

    nf-core/fastqrepair’s past year of commit activity
    Nextflow 2 MIT 2 0 1 Updated Feb 3, 2025
  • epitopeprediction Public

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

    nf-core/epitopeprediction’s past year of commit activity
    Nextflow 43 MIT 23 19 2 Updated Feb 3, 2025
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 1 2 36 10 Updated Feb 3, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 69 MIT 209 89 32 Updated Feb 3, 2025
  • stats Public
    nf-core/stats’s past year of commit activity
    HTML 0 0 16 10 Updated Feb 3, 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 291 MIT 749 460 (1 issue needs help) 186 Updated Feb 3, 2025
  • 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
    114 MIT 366 31 17 Updated Feb 3, 2025
  • multiplesequencealign Public

    A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.

    nf-core/multiplesequencealign’s past year of commit activity
    Nextflow 25 MIT 12 3 0 Updated Feb 3, 2025
  • variantbenchmarking Public

    A nextflow variant benchmarking pipeline - premature

    nf-core/variantbenchmarking’s past year of commit activity
    Nextflow 14 MIT 9 16 1 Updated Feb 3, 2025
  • createtaxdb Public

    Parallelised and automated construction of metagenomic classifier databases of different tools

    nf-core/createtaxdb’s past year of commit activity
    Nextflow 8 MIT 7 13 2 Updated Feb 3, 2025
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