Tools for working with SAM/BAM data
☆613Dec 22, 2024Updated last year
Alternatives and similar repositories for sambamba
Users that are interested in sambamba are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.☆243Aug 11, 2021Updated 5 years ago
- The next version of bwa-mem☆861Oct 15, 2025Updated 11 months ago
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,429Sep 10, 2026Updated last week
- C++ API & command-line toolkit for working with BAM data☆432May 18, 2025Updated last year
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆877May 2, 2026Updated 4 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.
- lumpy: a general probabilistic framework for structural variant discovery☆346Feb 22, 2026Updated 6 months ago
- bedtools - the swiss army knife for genome arithmetic☆1,049Jun 10, 2026Updated 3 months ago
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆536Updated this week
- Strelka2 germline and somatic small variant caller☆393Apr 20, 2026Updated 5 months ago
- A flexible framework for rapid genome analysis and interpretation☆320Oct 18, 2022Updated 3 years ago
- Tools for early stage alignment file processing☆96Mar 12, 2019Updated 7 years ago
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆337May 27, 2025Updated last year
- annotate a VCF with other VCFs/BEDs/tabixed files☆403Jun 16, 2026Updated 3 months ago
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,492Updated this week
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆878Sep 3, 2026Updated 2 weeks ago
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,957Sep 10, 2026Updated last week
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆685Mar 20, 2026Updated 6 months ago
- Structural variant and indel caller for mapped sequencing data☆467Oct 11, 2025Updated 11 months ago
- BEDOPS: high-performance genomic feature operations☆375Apr 29, 2025Updated last year
- A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.☆1,077Jul 31, 2026Updated last month
- Tools to process and analyze deep sequencing data.☆765Updated this week
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,249May 19, 2026Updated 4 months ago
- Official code repository for GATK versions 4 and up☆2,000Updated this week
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Copy number variant detection from targeted DNA sequencing☆616Aug 18, 2026Updated last month
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,767Aug 7, 2026Updated last month
- Count bases in BAM/CRAM files☆326Jul 10, 2026Updated 2 months ago
- The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants☆572Updated this week
- structural variant calling and genotyping with existing tools, but, smoothly.☆266Jun 17, 2024Updated 2 years ago
- Plot structural variant signals from many BAMs and CRAMs☆573Jul 13, 2024Updated 2 years ago
- Toolkit for processing sequences in FASTA/Q formats☆1,562Jun 1, 2025Updated last year
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,593Updated this week
- tools for adding mutations to existing .bam files, used for testing mutation callers☆252Aug 5, 2026Updated last month
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- A tool set for short variant discovery in genetic sequence data.☆207May 4, 2021Updated 5 years ago
- Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis☆1,030Aug 24, 2024Updated 2 years ago
- ☆98Jan 11, 2022Updated 4 years ago
- Variant calling and somatic mutation/CNV detection for next-generation sequencing data☆166Mar 28, 2023Updated 3 years ago
- A fast approximate aligner for long DNA sequences☆291Oct 11, 2024Updated last year
- BAM Statistics, Feature Counting and Annotation☆155Sep 10, 2026Updated last week
- fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome☆161Sep 9, 2026Updated last week