Graph-based alignment (Hierarchical Graph FM index)
☆541Jul 31, 2026Updated last month
Alternatives and similar repositories for hisat2
Users that are interested in hisat2 are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Transcript assembly and quantification for RNA-Seq☆534Aug 9, 2026Updated last month
- A fast and sensitive gapped read aligner☆812Sep 15, 2026Updated last week
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆500Jul 7, 2026Updated 2 months ago
- Near-optimal RNA-Seq quantification☆772Jul 12, 2026Updated 2 months ago
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,767Aug 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.
- Fast spliced aligner with low memory requirements☆40Sep 8, 2015Updated 11 years ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,249May 19, 2026Updated 4 months ago
- bedtools - the swiss army knife for genome arithmetic☆1,050Jun 10, 2026Updated 3 months ago
- RNA-seq aligner☆2,251Mar 18, 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.☆1,078Jul 31, 2026Updated last month
- The next version of bwa-mem☆863Oct 15, 2025Updated 11 months ago
- 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment☆932Updated this week
- SRA Tools☆1,368Sep 11, 2026Updated last week
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,959Updated this week
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Spliced read mapper for RNA-Seq☆92Jul 9, 2023Updated 3 years ago
- A fast multi-threaded k-mer counter☆552Mar 20, 2024Updated 2 years ago
- Trinity RNA-Seq de novo transcriptome assembly☆901Apr 23, 2026Updated 4 months ago
- Cutadapt removes adapter sequences from sequencing reads☆587Updated this week
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,430Sep 10, 2026Updated last week
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆479Aug 7, 2026Updated last month
- A quality control analysis tool for high throughput sequencing data☆618Aug 31, 2026Updated 3 weeks 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 2 weeks ago
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆289Jul 7, 2026Updated 2 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- A single molecule sequence assembler for genomes large and small.☆709Sep 10, 2026Updated last week
- Sequence-to-graph mapper and graph generator☆489Aug 11, 2025Updated last year
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,492Sep 15, 2026Updated last week
- Tools for working with SAM/BAM data☆613Dec 22, 2024Updated last year
- C library for high-throughput sequencing data formats☆951Updated this week
- RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.☆314Updated this week
- A fast approximate aligner for long DNA sequences☆291Oct 11, 2024Updated last year
- C++ API & command-line toolkit for working with BAM data☆432May 18, 2025Updated last year
- tools for working with genome variation graphs☆1,337Updated this week
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- ☆290Dec 29, 2025Updated 8 months ago
- Mummer alignment tool☆575Feb 4, 2025Updated last year
- An ultrafast memory-efficient short read aligner☆267May 11, 2022Updated 4 years ago
- Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads☆245Dec 29, 2023Updated 2 years ago
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆764Updated this week
- de Bruijn Graph-based read aligner☆36Sep 3, 2018Updated 8 years ago
- Program for aligning DNA sequences, a pairwise aligner.☆253May 20, 2026Updated 4 months ago