A Java API for high-throughput sequencing data (HTS) formats.
☆296Feb 25, 2026Updated last week
Alternatives and similar repositories for htsjdk
Users that are interested in htsjdk are comparing it to the libraries listed below
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.☆1,053Feb 4, 2026Updated last month
- C library for high-throughput sequencing data formats☆910Updated this week
- Official code repository for GATK versions 4 and up☆1,916Updated this week
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,855Feb 26, 2026Updated last week
- Assembly Based ReAligner☆75May 24, 2018Updated 7 years ago
- Specifications of SAM/BAM and related high-throughput sequencing file formats☆701Feb 24, 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…☆882Feb 2, 2026Updated last month
- Tools for working with SAM/BAM data☆606Dec 22, 2024Updated last year
- Java utilities for Bioinformatics☆518Feb 6, 2026Updated last month
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,710Mar 22, 2025Updated 11 months ago
- Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants …☆176Jan 7, 2020Updated 6 years ago
- Exploration of controlled loss of quality values for compressing CRAM files☆36Feb 23, 2023Updated 3 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…☆299Aug 22, 2018Updated 7 years ago
- Isaac Genome Alignment Software☆36Apr 7, 2015Updated 10 years ago
- VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications☆91Oct 3, 2024Updated last year
- Official code repository for GATK versions 1.0 through 3.7 (full licensed package). For GATK 4 code, see the https://github.com/broadinst…☆146Aug 22, 2018Updated 7 years ago
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆719Updated this week
- This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith…☆846Updated this week
- C++ API & command-line toolkit for working with BAM data☆429May 18, 2025Updated 9 months ago
- The next version of bwa-mem☆823Oct 15, 2025Updated 4 months ago
- A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.☆551May 15, 2025Updated 9 months ago
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆864Feb 8, 2026Updated 3 weeks ago
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆334May 27, 2025Updated 9 months ago
- samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.☆238Aug 11, 2021Updated 4 years ago
- Interactive in-browser track viewer☆280Oct 26, 2021Updated 4 years ago
- Experiments for "Scaling read aligners to hundreds of threads on general-purpose processors"☆11Jun 8, 2018Updated 7 years ago
- An RNA pipeline built on top of ADAM. Apache 2 licensed.☆19Jan 19, 2018Updated 8 years ago
- Processing WGS aDNA data using the ReichLab protocol☆13Mar 8, 2019Updated 6 years ago
- The nimble & robust variant annotator☆191Apr 25, 2024Updated last year
- Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale product…☆1,054Updated this week
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆669Oct 31, 2025Updated 4 months ago
- Toolkit for processing sequences in FASTA/Q formats☆1,531Jun 1, 2025Updated 9 months ago
- Toolkit to analyze genomic variation data, built on the GATK with Clojure☆66Nov 2, 2015Updated 10 years ago
- Note: tabix and bgzip binaries are now part of the HTSlib project.☆90Aug 3, 2021Updated 4 years ago
- lumpy: a general probabilistic framework for structural variant discovery☆338Feb 22, 2026Updated 2 weeks ago
- A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region exp…☆27Feb 23, 2026Updated last week
- Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis☆1,025Aug 24, 2024Updated last year
- bedtools - the swiss army knife for genome arithmetic☆1,025Mar 11, 2025Updated 11 months ago
- Reads simulator☆282Sep 3, 2021Updated 4 years ago