A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
☆1,066Jun 13, 2026Updated 3 weeks ago
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☆1,970Updated this week
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,754Jun 20, 2026Updated 2 weeks ago
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,918Jun 25, 2026Updated last week
- A Java API for high-throughput sequencing data (HTS) formats.☆300Jun 15, 2026Updated 3 weeks ago
- bedtools - the swiss army knife for genome arithmetic☆1,040Jun 10, 2026Updated 3 weeks ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- C library for high-throughput sequencing data formats☆933Updated 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.☆559May 15, 2025Updated last year
- RNA-seq aligner☆2,217Mar 18, 2025Updated last year
- Tools for working with SAM/BAM data☆612Dec 22, 2024Updated last year
- This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith…☆875Jun 23, 2026Updated 2 weeks ago
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,390Updated this week
- Graph-based alignment (Hierarchical Graph FM index)☆539Jan 27, 2026Updated 5 months ago
- C++ API & command-line toolkit for working with BAM data☆430May 18, 2025Updated last year
- Toolkit for processing sequences in FASTA/Q formats☆1,544Jun 1, 2025Updated last year
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- The next version of bwa-mem☆847Oct 15, 2025Updated 8 months ago
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆746Jul 1, 2026Updated last week
- Cutadapt removes adapter sequences from sequencing reads☆583Jun 26, 2026Updated last week
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆873Apr 20, 2026Updated 2 months ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,206May 19, 2026Updated last month
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,469Jun 29, 2026Updated last 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 7 years ago
- Specifications of SAM/BAM and related high-throughput sequencing file formats☆706Jun 4, 2026Updated last month
- A fast and sensitive gapped read aligner☆795Jun 1, 2026Updated last month
- 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.
- 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…☆897Jun 23, 2026Updated 2 weeks ago
- Mummer alignment tool☆564Feb 4, 2025Updated last year
- SRA Tools☆1,349Updated this week
- Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk…☆300Aug 22, 2018Updated 7 years ago
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆527Updated this week
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆472Apr 21, 2026Updated 2 months ago
- A quality control analysis tool for high throughput sequencing data☆605Jun 22, 2026Updated 2 weeks ago
- Strelka2 germline and somatic small variant caller☆393Apr 20, 2026Updated 2 months ago
- Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale product…☆1,070Jun 17, 2026Updated 3 weeks ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- BWK awk modified for biological data☆641Aug 11, 2022Updated 3 years ago
- Tools to process and analyze deep sequencing data.☆762Jun 24, 2026Updated 2 weeks ago
- Consistent adapter and quality trimming for NGS, with extra functionality for RRBS data☆564Jun 30, 2026Updated last week
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,574Jun 24, 2026Updated 2 weeks ago
- Trinity RNA-Seq de novo transcriptome assembly☆894Apr 23, 2026Updated 2 months ago
- Near-optimal RNA-Seq quantification☆766Mar 16, 2026Updated 3 months ago
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆682Mar 20, 2026Updated 3 months ago