Customizable workflows based on snakemake and python for the analysis of NGS data
☆404Oct 8, 2026Updated last week
Alternatives and similar repositories for snakepipes
Users that are interested in snakepipes are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- python module to plot beautiful and highly customizable genome browser tracks☆906Oct 3, 2026Updated last week
- Tools to process and analyze deep sequencing data.☆769Updated this week
- Sequana: a set of Snakemake NGS pipelines☆151Oct 5, 2026Updated last week
- RNA-seq workflow using STAR and DESeq2☆373Oct 7, 2026Updated last week
- This is the development home of the Snakemake wrapper repository, see☆254Oct 9, 2026Updated last week
- 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.
- Plot structural variant signals from many BAMs and CRAMs☆574Jul 13, 2024Updated 2 years ago
- This Snakemake pipeline implements the GATK best-practices workflow☆267Jun 8, 2023Updated 3 years ago
- This is the development home of the workflow management system Snakemake. For general information, see☆2,886Updated this week
- Differential ATAC-seq toolkit☆29Dec 21, 2023Updated 2 years ago
- ChIP-seq analysis notes from Ming Tang☆854Aug 5, 2024Updated 2 years ago
- RNAseq analysis notes from Ming Tang☆1,097Nov 15, 2021Updated 4 years ago
- TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files☆138Jan 28, 2026Updated 8 months ago
- A list of interesting genome browser and genome visualization programs☆1,110Updated this week
- Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).☆95Jul 18, 2017Updated 9 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Performant Pythonic GenomicRanges☆491Sep 23, 2026Updated 3 weeks ago
- Jupyter notebook based genomic data visualization toolkit.☆261Sep 22, 2026Updated 3 weeks ago
- SUPPA: Fast quantification of splicing and differential splicing☆307Nov 6, 2025Updated 11 months ago
- Detecting sites of genomic enrichment☆205Sep 20, 2026Updated 3 weeks ago
- genes and genomes at your fingertips☆410Jun 9, 2026Updated 4 months ago
- a snakemake pipeline to process ChIP-seq files from GEO or in-house☆133Jan 1, 2026Updated 9 months ago
- A tool to find sequencing data and metadata from public databases.☆604Aug 13, 2024Updated 2 years ago
- MACS -- Model-based Analysis of ChIP-Seq☆787Updated this week
- Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workf…☆168Jun 22, 2026Updated 3 months ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- Structural variant toolkit for VCFs☆426Oct 3, 2026Updated last week
- Quick mining and visualization of NGS data by integrating genomic databases☆272May 5, 2023Updated 3 years ago
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,442Oct 7, 2026Updated last week
- Fast and accurate gene fusion detection from RNA-Seq data☆280Sep 21, 2025Updated last year
- A snakemake pipeline for 10X genomics cellranger☆23Oct 13, 2025Updated last year
- Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis☆1,030Aug 24, 2024Updated 2 years ago
- A grammar of graphics for comparative genomics☆791Oct 5, 2026Updated last week
- Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data☆167Jun 14, 2026Updated 4 months ago
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,493Oct 6, 2026Updated last week
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- ATAC-seq snakemake pipeline☆90Feb 13, 2020Updated 6 years ago
- Package for fetching metadata and downloading data from SRA/ENA/GEO☆367Aug 16, 2026Updated 2 months ago
- Genome browser and variant annotation☆400Oct 8, 2026Updated last week
- RNA-Seq analysis workflow☆106Jul 14, 2021Updated 5 years ago
- Bioinformatics one liners from Ming Tang☆504Oct 4, 2020Updated 6 years ago
- A python extension for quick access to bigWig and bigBed files☆252Updated this week
- HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.☆279Sep 24, 2026Updated 3 weeks ago