Customizable workflows based on snakemake and python for the analysis of NGS data
☆399Jan 23, 2026Updated last month
Alternatives and similar repositories for snakepipes
Users that are interested in snakepipes are comparing it to the libraries listed below
Sorting:
- python module to plot beautiful and highly customizable genome browser tracks☆864Jul 10, 2024Updated last year
- Sequana: a set of Snakemake NGS pipelines☆152Updated this week
- Tools to process and analyze deep sequencing data.☆751Jul 23, 2025Updated 7 months ago
- This is the development home of the Snakemake wrapper repository, see☆239Feb 27, 2026Updated last week
- Plot structural variant signals from many BAMs and CRAMs☆560Jul 13, 2024Updated last year
- RNA-seq workflow using STAR and DESeq2☆352Dec 18, 2025Updated 2 months ago
- This Snakemake pipeline implements the GATK best-practices workflow☆262Jun 8, 2023Updated 2 years ago
- ChIP-seq analysis notes from Ming Tang☆842Aug 5, 2024Updated last year
- A tool to find sequencing data and metadata from public databases.☆596Aug 13, 2024Updated last year
- TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files☆136Jan 28, 2026Updated last month
- a snakemake pipeline to process ChIP-seq files from GEO or in-house☆131Jan 1, 2026Updated 2 months ago
- A list of interesting genome browser and genome visualization programs☆1,051Feb 25, 2026Updated last week
- Performant Pythonic GenomicRanges☆494Jan 27, 2026Updated last month
- SUPPA: Fast quantification of splicing and differential splicing☆293Nov 6, 2025Updated 4 months ago
- RNAseq analysis notes from Ming Tang☆1,069Nov 15, 2021Updated 4 years ago
- genes and genomes at your fingertips☆408Sep 30, 2025Updated 5 months ago
- Differential ATAC-seq toolkit☆28Dec 21, 2023Updated 2 years ago
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,297Jan 22, 2026Updated last month
- Fast and accurate gene fusion detection from RNA-Seq data☆262Sep 21, 2025Updated 5 months ago
- This is the development home of the workflow management system Snakemake. For general information, see☆2,718Feb 27, 2026Updated last week
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,425Feb 28, 2026Updated last week
- Jupyter notebook based genomic data visualization toolkit.☆250Dec 4, 2025Updated 3 months ago
- Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis☆1,025Aug 24, 2024Updated last year
- cython + htslib == fast VCF and BCF processing☆430Feb 23, 2026Updated last week
- Intervene: a tool for intersection and visualization of multiple genomic region and gene sets☆147Oct 28, 2023Updated 2 years ago
- Detecting sites of genomic enrichment☆199May 8, 2023Updated 2 years ago
- Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workf…☆168Feb 24, 2026Updated last week
- A grammar of graphics for comparative genomics☆744Feb 23, 2026Updated last week
- MACS -- Model-based Analysis of ChIP-Seq☆767Updated this week
- Structural variant toolkit for VCFs☆397Jan 23, 2026Updated last month
- Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).☆94Jul 18, 2017Updated 8 years ago
- Genome browser and variant annotation☆391Oct 30, 2025Updated 4 months ago
- A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, …☆88Updated this week
- RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.☆1,219Updated this week
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆828Feb 10, 2026Updated 3 weeks ago
- Bioinformatics one liners from Ming Tang☆501Oct 4, 2020Updated 5 years ago
- Package for fetching metadata and downloading data from SRA/ENA/GEO☆351Dec 9, 2025Updated 2 months ago
- Quick mining and visualization of NGS data by integrating genomic databases☆268May 5, 2023Updated 2 years ago
- A python extension for quick access to bigWig and bigBed files☆239Jan 14, 2026Updated last month