Customizable workflows based on snakemake and python for the analysis of NGS data
☆406Jul 22, 2026Updated this 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☆894Jul 10, 2024Updated 2 years ago
- Tools to process and analyze deep sequencing data.☆762Updated this week
- Sequana: a set of Snakemake NGS pipelines☆151Jul 2, 2026Updated 3 weeks ago
- RNA-seq workflow using STAR and DESeq2☆368Dec 18, 2025Updated 7 months ago
- This is the development home of the Snakemake wrapper repository, see☆249Updated this week
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Plot structural variant signals from many BAMs and CRAMs☆572Jul 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☆2,837Updated this week
- Differential ATAC-seq toolkit☆29Dec 21, 2023Updated 2 years ago
- ChIP-seq analysis notes from Ming Tang☆852Aug 5, 2024Updated last year
- RNAseq analysis notes from Ming Tang☆1,094Nov 15, 2021Updated 4 years ago
- TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files☆138Jan 28, 2026Updated 5 months ago
- A list of interesting genome browser and genome visualization programs☆1,098Updated this week
- Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).☆95Jul 18, 2017Updated 9 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Performant Pythonic GenomicRanges☆494Apr 23, 2026Updated 3 months ago
- Jupyter notebook based genomic data visualization toolkit.☆259Jun 8, 2026Updated last month
- SUPPA: Fast quantification of splicing and differential splicing☆306Nov 6, 2025Updated 8 months ago
- Detecting sites of genomic enrichment☆202May 8, 2023Updated 3 years ago
- genes and genomes at your fingertips☆412Jun 9, 2026Updated last month
- a snakemake pipeline to process ChIP-seq files from GEO or in-house☆133Jan 1, 2026Updated 6 months ago
- A tool to find sequencing data and metadata from public databases.☆601Aug 13, 2024Updated last year
- MACS -- Model-based Analysis of ChIP-Seq☆781Jul 7, 2026Updated 2 weeks ago
- Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workf…☆169Jun 22, 2026Updated last month
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Structural variant toolkit for VCFs☆420May 22, 2026Updated 2 months ago
- Quick mining and visualization of NGS data by integrating genomic databases☆273May 5, 2023Updated 3 years ago
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,400Jul 10, 2026Updated 2 weeks ago
- Fast and accurate gene fusion detection from RNA-Seq data☆273Sep 21, 2025Updated 10 months ago
- Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis☆1,030Aug 24, 2024Updated last year
- A grammar of graphics for comparative genomics☆774Jul 3, 2026Updated 3 weeks ago
- Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data☆167Jun 14, 2026Updated last month
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,480Updated this week
- ATAC-seq snakemake pipeline☆91Feb 13, 2020Updated 6 years 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.
- A snakemake pipeline for 10X genomics cellranger☆23Oct 13, 2025Updated 9 months ago
- Package for fetching metadata and downloading data from SRA/ENA/GEO☆368Jul 13, 2026Updated 2 weeks ago
- Genome browser and variant annotation☆396Jun 25, 2026Updated last month
- RNA-Seq analysis workflow☆106Jul 14, 2021Updated 5 years ago
- Bioinformatics one liners from Ming Tang☆501Oct 4, 2020Updated 5 years ago
- A python extension for quick access to bigWig and bigBed files☆248Updated this week
- HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.☆275Jul 17, 2025Updated last year