A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
☆1,077Jul 31, 2026Updated last month
Alternatives and similar repositories for picard
Users that are interested in picard are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Official code repository for GATK versions 4 and up☆1,995Updated this week
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,767Aug 7, 2026Updated last month
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,950Updated this week
- A Java API for high-throughput sequencing data (HTS) formats.☆303Updated this week
- bedtools - the swiss army knife for genome arithmetic☆1,047Jun 10, 2026Updated 2 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.
- C library for high-throughput sequencing data formats☆949Updated this week
- A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.☆564May 15, 2025Updated last year
- RNA-seq aligner☆2,244Mar 18, 2025Updated last year
- This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith…☆889Updated this week
- Tools for working with SAM/BAM data☆614Dec 22, 2024Updated last year
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,424Updated this week
- Graph-based alignment (Hierarchical Graph FM index)☆539Jul 31, 2026Updated last month
- C++ API & command-line toolkit for working with BAM data☆432May 18, 2025Updated last year
- Toolkit for processing sequences in FASTA/Q formats☆1,559Jun 1, 2025Updated last year
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- The next version of bwa-mem☆862Oct 15, 2025Updated 10 months ago
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆758Aug 6, 2026Updated last month
- Cutadapt removes adapter sequences from sequencing reads☆587Jul 27, 2026Updated last month
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,245May 19, 2026Updated 3 months ago
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆877Updated this week
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,492Updated this week
- Official code repository for GATK versions 1.0 through 3.7 (full licensed package). For GATK 4 code, see the https://github.com/broadinst…☆147Aug 22, 2018Updated 8 years ago
- A fast and sensitive gapped read aligner☆811Jun 1, 2026Updated 3 months ago
- Specifications of SAM/BAM and related high-throughput sequencing file formats☆711Aug 25, 2026Updated last week
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- SRA Tools☆1,365Updated this week
- Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight…☆911Updated this week
- Mummer alignment tool☆574Feb 4, 2025Updated last year
- Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk…☆302Aug 22, 2018Updated 8 years ago
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆535Updated this week
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆477Aug 7, 2026Updated last month
- Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale product…☆1,080Updated this week
- A quality control analysis tool for high throughput sequencing data☆615Aug 31, 2026Updated last week
- Strelka2 germline and somatic small variant caller☆394Apr 20, 2026Updated 4 months ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- BWK awk modified for biological data☆643Aug 11, 2022Updated 4 years ago
- Consistent adapter and quality trimming for NGS, with extra functionality for RRBS data☆576Updated this week
- Trinity RNA-Seq de novo transcriptome assembly☆898Apr 23, 2026Updated 4 months ago
- Tools to process and analyze deep sequencing data.☆765Updated this week
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,590Updated this week
- Near-optimal RNA-Seq quantification☆769Jul 12, 2026Updated last month
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆684Mar 20, 2026Updated 5 months ago