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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 252 199

  2. modules modules Public

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

    Nextflow 297 785

  3. rnaseq rnaseq Public

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

    Nextflow 1k 741

  4. sarek sarek Public

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

    Nextflow 432 436

Repositories

Showing 10 of 157 repositories
  • coproid Public

    Coprolite host Identification pipeline

    nf-core/coproid’s past year of commit activity
    Nextflow 9 MIT 4 2 0 Updated Mar 24, 2025
  • bactmap Public

    A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

    nf-core/bactmap’s past year of commit activity
    Nextflow 53 MIT 39 43 (1 issue needs help) 0 Updated Mar 24, 2025
  • viralrecon Public

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

    nf-core/viralrecon’s past year of commit activity
    Nextflow 133 MIT 121 31 (4 issues need help) 5 Updated Mar 24, 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
    117 MIT 369 31 10 Updated Mar 24, 2025
  • references Public

    nf-core/references is a bioinformatics pipeline that build references, for multiple use cases

    nf-core/references’s past year of commit activity
    Nextflow 11 MIT 4 22 0 Updated Mar 24, 2025
  • proteinfamilies Public

    Generation and update of protein families

    nf-core/proteinfamilies’s past year of commit activity
    Nextflow 11 MIT 1 14 1 Updated Mar 24, 2025
  • taxprofiler Public

    Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

    nf-core/taxprofiler’s past year of commit activity
    Nextflow 139 MIT 46 40 (1 issue needs help) 5 Updated Mar 24, 2025
  • demo Public

    nf-core/demo is a simple nf-core style bioinformatics pipeline for workshops and demos.

    nf-core/demo’s past year of commit activity
    Nextflow 3 MIT 8 3 1 Updated Mar 24, 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 21 (1 issue needs help) 1 Updated Mar 24, 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 783 533 (1 issue needs help) 133 Updated Mar 24, 2025
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