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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 247 193

  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 974 718

  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
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag’s past year of commit activity
    Nextflow 226 MIT 118 62 (1 issue needs help) 13 Updated Feb 5, 2025
  • configs Public

    Config files used to define parameters specific to compute environments at different Institutions

    nf-core/configs’s past year of commit activity
    Nextflow 93 MIT 284 12 16 Updated Feb 5, 2025
  • genomeassembler Public
    nf-core/genomeassembler’s past year of commit activity
    Nextflow 16 MIT 13 39 (1 issue needs help) 2 Updated Feb 5, 2025
  • proteinfamilies Public

    Generation and update of protein families

    nf-core/proteinfamilies’s past year of commit activity
    Nextflow 2 MIT 1 0 2 Updated Feb 5, 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 135 MIT 39 41 (1 issue needs help) 7 Updated Feb 5, 2025
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 1 2 35 10 Updated Feb 5, 2025
  • variantbenchmarking Public

    A nextflow variant benchmarking pipeline - premature

    nf-core/variantbenchmarking’s past year of commit activity
    Nextflow 14 MIT 9 15 2 Updated Feb 5, 2025
  • funcscan Public

    (Meta-)genome screening for functional and natural product gene sequences

    nf-core/funcscan’s past year of commit activity
    Nextflow 78 MIT 22 17 2 Updated Feb 5, 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) 188 Updated Feb 5, 2025
  • pairgenomealign Public

    Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results

    nf-core/pairgenomealign’s past year of commit activity
    Nextflow 6 MIT 3 13 1 Updated Feb 5, 2025
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