Graph-based alignment (Hierarchical Graph FM index)
☆530Jan 27, 2026Updated last month
Alternatives and similar repositories for hisat2
Users that are interested in hisat2 are comparing it to the libraries listed below
Sorting:
- Transcript assembly and quantification for RNA-Seq☆489Dec 26, 2025Updated 2 months ago
- A fast and sensitive gapped read aligner☆773Feb 17, 2026Updated 2 weeks ago
- Near-optimal RNA-Seq quantification☆724Updated this week
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆462Dec 26, 2024Updated last year
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,128Feb 13, 2026Updated 2 weeks ago
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,707Mar 22, 2025Updated 11 months ago
- bedtools - the swiss army knife for genome arithmetic☆1,025Mar 11, 2025Updated 11 months ago
- RNA-seq aligner☆2,146Mar 18, 2025Updated 11 months ago
- The next version of bwa-mem☆819Oct 15, 2025Updated 4 months ago
- 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 3 weeks ago
- 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment☆862May 29, 2024Updated last year
- SRA Tools☆1,309Updated this week
- A fast multi-threaded k-mer counter☆529Mar 20, 2024Updated last year
- Fast spliced aligner with low memory requirements☆41Sep 8, 2015Updated 10 years ago
- Cutadapt removes adapter sequences from sequencing reads☆572Jan 12, 2026Updated last month
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,292Jan 22, 2026Updated last month
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,849Feb 24, 2026Updated last week
- Spliced read mapper for RNA-Seq☆92Jul 9, 2023Updated 2 years ago
- C++ API & command-line toolkit for working with BAM data☆429May 18, 2025Updated 9 months ago
- Mummer alignment tool☆550Feb 4, 2025Updated last year
- ☆285Dec 29, 2025Updated 2 months ago
- Trinity RNA-Seq de novo transcriptome assembly☆883Feb 7, 2025Updated last year
- Tools for working with SAM/BAM data☆605Dec 22, 2024Updated last year
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,425Updated this week
- A quality control analysis tool for high throughput sequencing data☆585Jan 5, 2026Updated last month
- tools for working with genome variation graphs☆1,300Updated this week
- Program for aligning DNA sequences, a pairwise aligner.☆240Jun 16, 2025Updated 8 months ago
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆262Jul 12, 2025Updated 7 months ago
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆461Updated this week
- Sequence-to-graph mapper and graph generator☆470Aug 11, 2025Updated 6 months ago
- C library for high-throughput sequencing data formats☆910Feb 6, 2026Updated 3 weeks ago
- A fast approximate aligner for long DNA sequences☆287Oct 11, 2024Updated last year
- Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads☆238Dec 29, 2023Updated 2 years ago
- A single molecule sequence assembler for genomes large and small.☆695Feb 24, 2026Updated last week
- RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.☆293Dec 17, 2025Updated 2 months ago
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆718Updated this 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
- Strelka2 germline and somatic small variant caller☆390Dec 29, 2021Updated 4 years ago
- Ultrafast de novo assembly for long noisy reads (though having no consensus step)☆352Jul 19, 2025Updated 7 months ago