nf-core/references is a bioinformatics pipeline that build references, for multiple use cases
☆22Aug 27, 2026Updated this week
Alternatives and similar repositories for references
Users that are interested in references are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Automatically source dotenv files into your Nextflow scope☆10Mar 27, 2026Updated 5 months ago
- ☆13Aug 10, 2026Updated 2 weeks ago
- A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets☆13Aug 17, 2026Updated last week
- nf-test utility functions☆13Updated this week
- A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data☆13Aug 4, 2026Updated 3 weeks ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- A VSCode extension pack for nf-core developers.☆15Mar 7, 2025Updated last year
- Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research☆51Aug 19, 2026Updated last week
- Cancer Predisposition Sequencing Reporter (CPSR)☆67Aug 16, 2026Updated 2 weeks ago
- This repository hosts a large collection of Nextflow snippets☆56Jan 26, 2025Updated last year
- Analysis pipeline to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and …☆22Updated this week
- Testing building mulled containers for multi-requirement tools.☆85Updated this week
- Test data for MultiQC.☆24Updated this week
- Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and gro…☆28Aug 20, 2026Updated last week
- A Nextflow pipeline to play Doom☆10Dec 1, 2025Updated 8 months ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- High-performance UMI tools for NGS data analysis☆52Updated this week
- Merge and compare structural variants across callers, samples, and platforms. Standardizes BND-heavy output from GRIDSS, SvABA, Sniffles,…☆47Aug 16, 2026Updated 2 weeks ago
- Recommendations to contenarized your bioinformatics software☆12May 30, 2018Updated 8 years ago
- Spiritual successor to picard for sequencing qc☆62Jul 19, 2026Updated last month
- An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.☆71Updated this week
- Nextflow runs monitoring and organisation UI☆78Sep 20, 2024Updated last year
- A collection of Groovy classes that provide utility services to nextflow pipelines.☆13Oct 25, 2022Updated 3 years ago
- Blazingly fast, streaming duplicate detection for NGS data☆21Updated this week
- A bioinformatics pipeline to phase and impute genetic data☆33Jul 27, 2026Updated last month
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- A repository for the schemas used for the Data Repository Service.☆64Aug 10, 2026Updated 2 weeks ago
- Differential gene expression analysis and pathway analysis of RNAseq data☆32Jul 3, 2025Updated last year
- Generate beautiful API documentation for Nextflow pipelines☆19Aug 9, 2026Updated 3 weeks ago
- Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq☆95Updated this week
- A Rust library for storing generic genomic data by sorted chromosome name☆18Sep 26, 2024Updated last year
- A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region exp…☆28Jun 25, 2026Updated 2 months ago
- CLI tool to verify workflow reproducibility☆17Jan 29, 2024Updated 2 years ago
- A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.☆41Jul 27, 2026Updated last month
- Python implementation and field-tool for automated pipeline launching through Tower CLI (beta)☆36Aug 10, 2026Updated 2 weeks ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Nextflow plugin to render provenance reports for pipeline runs. Supports standard formats such as BioCompute Object and Workflow Run RO-C…☆30May 17, 2026Updated 3 months ago
- Bioinformatics pipeline to identify differentially active transcription factors between conditions using expression and epigenetic data☆14Mar 12, 2024Updated 2 years ago
- Simple test framework for Nextflow pipelines☆190Apr 27, 2026Updated 4 months ago
- Snakemake workflow for somatic mutation detection without matched normal samples☆14Mar 4, 2023Updated 3 years ago
- Search for a set of compatible indexes for your sequencing experiment☆11Sep 6, 2019Updated 6 years ago
- Generate random test data for bioinformatics☆27Jun 17, 2024Updated 2 years ago
- An analysis pipeline for Nanostring nCounter expression data.☆18Jul 28, 2026Updated last month