A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
☆1,081Jul 31, 2026Updated 2 months 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☆2,007Updated this week
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,768Aug 7, 2026Updated 2 months ago
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,968Updated this week
- A Java API for high-throughput sequencing data (HTS) formats.☆303Updated this week
- bedtools - the swiss army knife for genome arithmetic☆1,053Jun 10, 2026Updated 4 months ago
- 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.
- C library for high-throughput sequencing data formats☆955Updated 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.☆565May 15, 2025Updated last year
- RNA-seq aligner☆2,266Mar 18, 2025Updated last year
- Tools for working with SAM/BAM data☆613Dec 22, 2024Updated last year
- This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith…☆898Sep 30, 2026Updated 2 weeks ago
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,444Oct 7, 2026Updated last week
- Graph-based alignment (Hierarchical Graph FM index)☆542Jul 31, 2026Updated 2 months ago
- C++ API & command-line toolkit for working with BAM data☆432May 18, 2025Updated last year
- Toolkit for processing sequences in FASTA/Q formats☆1,564Jun 1, 2025Updated last year
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆768Updated this week
- The next version of bwa-mem☆865Oct 15, 2025Updated last year
- Cutadapt removes adapter sequences from sequencing reads☆588Sep 21, 2026Updated 3 weeks ago
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆881Sep 3, 2026Updated last month
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,260May 19, 2026Updated 4 months ago
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,494Oct 6, 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 8 years ago
- Specifications of SAM/BAM and related high-throughput sequencing file formats☆715Aug 25, 2026Updated last month
- A fast and sensitive gapped read aligner☆810Sep 22, 2026Updated 3 weeks ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- SRA Tools☆1,371Oct 7, 2026Updated last 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☆576Feb 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…☆303Aug 22, 2018Updated 8 years ago
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆479Aug 7, 2026Updated 2 months ago
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆537Oct 5, 2026Updated last week
- Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale product…☆1,085Updated this week
- A quality control analysis tool for high throughput sequencing data☆624Oct 7, 2026Updated last week
- Strelka2 germline and somatic small variant caller☆393Apr 20, 2026Updated 5 months ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Consistent adapter and quality trimming for NGS, with extra functionality for RRBS data☆579Updated this week
- Tools to process and analyze deep sequencing data.☆769Updated this week
- BWK awk modified for biological data☆643Aug 11, 2022Updated 4 years ago
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,597Sep 24, 2026Updated 3 weeks ago
- Trinity RNA-Seq de novo transcriptome assembly☆902Apr 23, 2026Updated 5 months ago
- Near-optimal RNA-Seq quantification☆775Jul 12, 2026Updated 3 months ago
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆686Oct 2, 2026Updated 2 weeks ago