HISAT2 is command-line software for aligning DNA and RNA sequencing reads to reference genomes, including graph indexes representing human genetic variation.
The project documents graph-based and splice-aware alignment, reference-index building, SAM output, and APIs. It is free under GPLv3, but requires command-line installation and local compute. Public review-platform ratings and recurring user-review themes were not verified.
This profile combines documented product information and independent evidence where available. It is not a hands-on test unless TechZella explicitly identifies one.
HISAT2 is command-line software for mapping next-generation DNA and RNA sequencing reads to a reference genome or a population of human genomes. It uses a Hierarchical Graph FM index, combining a global graph index with local indexes.
It outputs alignments in SAM format, which supports downstream use with tools such as SAMtools and GATK. HISAT2 is free under GPL-3.0 and runs locally rather than as a hosted application.
A quick way to understand who this product may suit, where its limits matter, and which facts are most relevant before you compare alternatives.
Research teams aligning short-read DNA or RNA sequencing data to a reference genome, especially when graph indexes for human variation or splice-aware RNA alignment are relevant.
Buyers seeking a hosted graphical application, vendor-managed support, or a turnkey clinical workflow should assess other tools; HISAT2 is a command-line program distributed as open-source software, and should evaluate alternatives such as STAR instead.
API, CLI, Linux, macOS, Windows
7.4/10
These are the product-specific differences that may matter when deciding whether the software fits your workflow. They are based on documented evidence rather than a universal ranking.
These are documented constraints or practical friction points that may matter before you adopt the product.
Users should check the release repository and confirm which version their package or deployment actually installs rather than assuming the download page is current.
Evidence source ↗Windows users may need to install and configure a compiler environment before deployment.
Evidence source ↗HISAT2 is distributed under the GPL-3.0 license. Compute, storage, installation, and operational costs are not included.
Check current pricing →Pricing may change. Verify current plans on the vendor's website.
Compare similar products directly, then see which alternatives may make more sense when your requirements differ.
| Decision factor | HISAT2 | STAR | Bowtie 2 |
|---|---|---|---|
| Core scope | Maps next-generation sequencing reads, including DNA and RNA, to population or single-reference genomes using graph FM indexing. | A spliced RNA-seq aligner for mapping transcripts to a reference. Source ↗ | Aligns sequencing reads to long references with gapped, local, and paired-end modes; its manual does not describe splice-aware RNA alignment as its core scope. Source ↗ |
| Deployment | Command-line software; Linux and macOS binaries are listed, and the manual documents Windows source builds. | Command-line software with documented 64-bit Linux and macOS requirements and executables. Source ↗ | Command-line software with documented Linux, macOS, Windows, and BSD support. Source ↗ |
| Pricing model | Open source under GPL-3.0. | Open source under the MIT License. Source ↗ | Open source under GPLv3. Source ↗ |
Only factors supported by the available research are shown. The comparison is descriptive, not a ranking.
These products address broadly similar requirements. The descriptions focus on documented reasons a buyer might compare them with HISAT2.
| License | GPL-3.0 |
|---|---|
| Latest release found | 2.2.3, July 31, 2026 |
| Interface | Command line |
| Output format | SAM |
| Documented operating systems | Linux, macOS, Windows |
| Prebuilt binaries listed | Linux x86_64 and macOS x86_64 |
| Minimum memory in repository guidance | 8 GB RAM |
| APIs | C++, Python, Java |
| Documented interoperability | SAMtools, GATK |
| Hosting | Self-installed; hosted service not documented |
Verified installation, hosting, administration, or environment details that can affect implementation.
| Installation or hosting | Command-line software installed and run locally; documented build routes include Linux, macOS, and Windows toolchains. No hosted service is documented. Source ↗ |
|---|---|
| Architecture and minimum requirements | The repository states a 64-bit Linux or Mac OS X computer and at least 8 GB RAM; the manual also covers Windows source builds. Source ↗ |
Documented portability, standards, export, or switching considerations. No switching-cost score is shown unless the evidence supports one.
HISAT2 writes alignments in SAM format, which the manual identifies as interoperable with tools such as SAMtools and GATK.
Evidence source ↗Indexes are built from reference sequence files or downloaded as prebuilt HISAT2 indexes. The project documents HISAT2-specific index files, so teams switching aligners should plan to create or obtain compatible indexes.
Evidence source ↗A proprietary editorial score based on product capabilities, usability, value, performance, support and user sentiment evidence.
The project documents graph-based and splice-aware alignment, reference-index building, SAM output, and APIs. It is free under GPLv3, but requires command-line installation and local compute. Public review-platform ratings and recurring user-review themes were not verified.
Methodology v1.0. The assessment weighs feature coverage (25%), ease of use (15%), value for money (20%), performance (15%), support (10%) and user sentiment (15%), using researched product evidence and verified review evidence where available. It is a TechZella editorial assessment, not a direct user-review average.
Key claims are linked to the sources used to verify them. This evidence record is separate from third-party user ratings.
TechZella evaluates software using documented product capabilities, pricing information, usability and value considerations, independent user evidence where available, and competitive context. The assessment is an editorial review, not a hands-on test unless one is explicitly identified. Our editorial assessment is based on 4 documented sources.
The project site describes mapping next-generation DNA and RNA reads to a population of human genomes as well as a single reference genome.
View source ↗Verified 2026-11-11The project describes a global graph FM index combined with local indexes as its HGFM indexing approach.
View source ↗Verified 2026-11-11The manual states both the output format and license, and describes command-line operation across operating systems.
View source ↗Verified 2026-11-11The official site describes APIs for retrieving genomic locations from repeat alignments for downstream analyses.
View source ↗Verified 2026-11-11The GitHub release page identifies version 2.2.3, dated July 31, 2026, and lists ARM compilation support using sse2neon.
View source ↗Verified 2026-11-11The study reports results for six aligners using 48 grapevine powdery mildew samples and notes that results can vary with species and data.
View source ↗Verified 2026-11-11Answers begin with the clearest available response, followed by the context that helps you act on it.
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