A Java API for high-throughput sequencing data (HTS) formats.
☆302Jul 26, 2026Updated this week
Alternatives and similar repositories for htsjdk
Users that are interested in htsjdk are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.☆1,069Jun 13, 2026Updated last month
- C library for high-throughput sequencing data formats☆939Updated this week
- Official code repository for GATK versions 4 and up☆1,978Updated this week
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,932Updated this week
- Processing WGS aDNA data using the ReichLab protocol☆13Mar 8, 2019Updated 7 years ago
- 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.
- 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☆709Jul 20, 2026Updated last week
- Tools for working with SAM/BAM data☆613Dec 22, 2024Updated last year
- 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…☆902Jul 19, 2026Updated last week
- Java utilities for Bioinformatics☆525Updated this week
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆756Updated this week
- Exploration of controlled loss of quality values for compressing CRAM files☆36Feb 23, 2023Updated 3 years ago
- Assembly Based ReAligner☆75May 24, 2018Updated 8 years ago
- samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.☆243Aug 11, 2021Updated 4 years ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale product…☆1,077Jul 16, 2026Updated last week
- Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants …☆178Jan 7, 2020Updated 6 years ago
- Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk…☆301Aug 22, 2018Updated 7 years ago
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,759Updated this week
- BigWIG, BigBED and TDF for the JVM☆13Feb 23, 2021Updated 5 years ago
- A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.☆562May 15, 2025Updated last year
- A command-line tool for executing, managing, and querying WDL workflows on Cromwell servers.☆14Aug 17, 2018Updated 7 years ago
- C++ API & command-line toolkit for working with BAM data☆432May 18, 2025Updated last year
- The nimble & robust variant annotator☆197Apr 20, 2026Updated 3 months ago
- 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.
- Experiments for "Scaling read aligners to hundreds of threads on general-purpose processors"☆11Jun 8, 2018Updated 8 years ago
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆338May 27, 2025Updated last year
- VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications☆93Oct 3, 2024Updated last year
- The next version of bwa-mem☆853Oct 15, 2025Updated 9 months ago
- Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead☆32Aug 16, 2017Updated 8 years ago
- This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith…☆880Updated this week
- Text Only Genome Viewer!☆249May 14, 2026Updated 2 months ago
- Canvas - Copy number variant (CNV) calling from DNA sequencing data☆129Apr 20, 2026Updated 3 months ago
- fastx-utils using klib☆19Sep 1, 2020Updated 5 years ago
- 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.
- A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region exp…☆27Jun 25, 2026Updated last month
- CLI for interacting with Cromwell servers☆54Apr 2, 2024Updated 2 years ago
- Toolkit for processing sequences in FASTA/Q formats☆1,550Jun 1, 2025Updated last year
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆876Apr 20, 2026Updated 3 months ago
- Note: tabix and bgzip binaries are now part of the HTSlib project.☆92Aug 3, 2021Updated 4 years ago
- Tools for early stage alignment file processing☆96Mar 12, 2019Updated 7 years ago
- Java Bindings (JNI) for bwa☆20Dec 15, 2016Updated 9 years ago