Skip to content
@nf-core

nf-core

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

Pinned Loading

  1. tools tools Public

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

    Python 246 192

  2. modules modules Public

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

    Nextflow 290 743

  3. rnaseq rnaseq Public

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

    Nextflow 965 719

  4. sarek sarek Public

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

    Nextflow 416 421

  5. chipseq chipseq Public

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

    Nextflow 203 149

  6. eager eager Public

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

    Nextflow 155 82

Repositories

Showing 10 of 150 repositories
  • 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 10 1 Updated Jan 23, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 70 MIT 207 90 33 Updated Jan 23, 2025
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 14 MIT 6 9 5 Updated Jan 24, 2025
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 246 MIT 192 270 42 Updated Jan 23, 2025
  • pathogensurveillance Public

    Surveillance of pathogens using population genomics and sequencing

    nf-core/pathogensurveillance’s past year of commit activity
    Nextflow 15 MIT 6 43 (2 issues need help) 0 Updated Jan 23, 2025
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 1 2 45 8 Updated Jan 23, 2025
  • 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 1 MIT 2 5 1 Updated Jan 23, 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 92 MIT 282 12 15 Updated Jan 23, 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 290 MIT 743 459 (1 issue needs help) 177 Updated Jan 23, 2025
  • riboseq Public

    Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.

    nf-core/riboseq’s past year of commit activity
    Nextflow 12 MIT 8 15 2 Updated Jan 23, 2025
View all repositories

Top languages

Loading…

Most used topics

Loading…