Customizable workflows based on snakemake and python for the analysis of NGS data
☆404May 5, 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☆879Jul 10, 2024Updated last year
- Tools to process and analyze deep sequencing data.☆759Jul 23, 2025Updated 9 months ago
- Sequana: a set of Snakemake NGS pipelines☆151Apr 15, 2026Updated 3 weeks ago
- RNA-seq workflow using STAR and DESeq2☆357Dec 18, 2025Updated 4 months ago
- This is the development home of the Snakemake wrapper repository, see☆243Updated this week
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- Plot structural variant signals from many BAMs and CRAMs☆567Jul 13, 2024Updated last year
- This Snakemake pipeline implements the GATK best-practices workflow☆264Jun 8, 2023Updated 2 years ago
- This is the development home of the workflow management system Snakemake. For general information, see☆2,770Updated this week
- Differential ATAC-seq toolkit☆29Dec 21, 2023Updated 2 years ago
- ChIP-seq analysis notes from Ming Tang☆851Aug 5, 2024Updated last year
- RNAseq analysis notes from Ming Tang☆1,082Nov 15, 2021Updated 4 years ago
- TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files☆136Jan 28, 2026Updated 3 months ago
- A list of interesting genome browser and genome visualization programs☆1,070Updated this week
- Jupyter notebook based genomic data visualization toolkit.☆257Dec 4, 2025Updated 5 months ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Performant Pythonic GenomicRanges☆495Apr 23, 2026Updated 2 weeks ago
- genes and genomes at your fingertips☆412Mar 5, 2026Updated 2 months ago
- a snakemake pipeline to process ChIP-seq files from GEO or in-house☆132Jan 1, 2026Updated 4 months ago
- SUPPA: Fast quantification of splicing and differential splicing☆298Nov 6, 2025Updated 6 months ago
- Detecting sites of genomic enrichment☆201May 8, 2023Updated 2 years ago
- Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).☆94Jul 18, 2017Updated 8 years ago
- A tool to find sequencing data and metadata from public databases.☆597Aug 13, 2024Updated last year
- MACS -- Model-based Analysis of ChIP-Seq☆774Apr 8, 2026Updated 3 weeks ago
- Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workf…☆170Feb 24, 2026Updated 2 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Structural variant toolkit for VCFs☆407Mar 21, 2026Updated last month
- 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...)☆2,351Apr 24, 2026Updated last week
- Fast and accurate gene fusion detection from RNA-Seq data☆270Sep 21, 2025Updated 7 months ago
- A grammar of graphics for comparative genomics☆762Feb 23, 2026Updated 2 months ago
- Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data☆166Oct 2, 2025Updated 7 months ago
- Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis☆1,029Aug 24, 2024Updated last year
- ATAC-seq snakemake pipeline☆90Feb 13, 2020Updated 6 years ago
- A snakemake pipeline for 10X genomics cellranger☆22Oct 13, 2025Updated 6 months 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.
- Package for fetching metadata and downloading data from SRA/ENA/GEO☆357Dec 9, 2025Updated 4 months ago
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,446Apr 24, 2026Updated last week
- Genome browser and variant annotation☆392Apr 28, 2026Updated last week
- RNA-Seq analysis workflow☆105Jul 14, 2021Updated 4 years ago
- Bioinformatics one liners from Ming Tang☆500Oct 4, 2020Updated 5 years ago
- A python extension for quick access to bigWig and bigBed files☆243Jan 14, 2026Updated 3 months ago
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆847Apr 24, 2026Updated last week