C++ API & command-line toolkit for working with BAM data
☆432May 18, 2025Updated last year
Alternatives and similar repositories for bamtools
Users that are interested in bamtools are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Tools for working with SAM/BAM data☆613Dec 22, 2024Updated last year
- bedtools - the swiss army knife for genome arithmetic☆1,054Jun 10, 2026Updated 3 months ago
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆686Oct 2, 2026Updated last week
- C++ htslib/bwa-mem/fermi interface for interrogating sequence data☆139Apr 27, 2026Updated 5 months ago
- C library for high-throughput sequencing data formats☆953Updated this week
- 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.
- 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
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,965Updated this week
- Strelka2 germline and somatic small variant caller☆393Apr 20, 2026Updated 5 months ago
- Tools for early stage alignment file processing☆96Mar 12, 2019Updated 7 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.☆565May 15, 2025Updated last year
- Cutadapt removes adapter sequences from sequencing reads☆587Sep 21, 2026Updated 2 weeks ago
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆881Sep 3, 2026Updated last month
- de novo sequence assembler using string graphs☆244Aug 8, 2019Updated 7 years ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,254May 19, 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.
- The next version of bwa-mem☆862Oct 15, 2025Updated 11 months ago
- A method for variant graph genotyping based on exact alignment of k-mers☆88Apr 1, 2019Updated 7 years ago
- ☆98Jan 11, 2022Updated 4 years ago
- SeqAn's official repository.☆502Aug 11, 2026Updated last month
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,769Aug 7, 2026Updated 2 months ago
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆537Oct 1, 2026Updated last week
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆768Updated this week
- NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on r…☆310Mar 18, 2024Updated 2 years ago
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆878May 2, 2026Updated 5 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Tools for bam file processing☆56Apr 20, 2015Updated 11 years ago
- Specifications of SAM/BAM and related high-throughput sequencing file formats☆714Aug 25, 2026Updated last month
- annotate a VCF with other VCFs/BEDs/tabixed files☆403Jun 16, 2026Updated 3 months ago
- samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.☆243Aug 11, 2021Updated 5 years ago
- goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary☆227Sep 18, 2025Updated last year
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆502Jul 7, 2026Updated 3 months ago
- Graph-based alignment (Hierarchical Graph FM index)☆542Jul 31, 2026Updated 2 months ago
- ☆291Dec 29, 2025Updated 9 months ago
- 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…☆911Sep 7, 2026Updated last month
- 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.
- A powerful toolset for genome arithmetic.☆143May 28, 2021Updated 5 years ago
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆337May 27, 2025Updated last year
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,492Oct 2, 2026Updated last week
- BEDOPS: high-performance genomic feature operations☆375Apr 29, 2025Updated last year
- Reads simulator☆290Sep 3, 2021Updated 5 years ago
- 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment☆936Updated this week
- Tools to process and analyze deep sequencing data.☆768Sep 27, 2026Updated last week