🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
☆925Aug 11, 2026Updated this week
Alternatives and similar repositories for salmon
Users that are interested in salmon are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Near-optimal RNA-Seq quantification☆769Jul 12, 2026Updated last month
- Differential analysis of RNA-Seq☆316May 28, 2025Updated last year
- RNA-seq aligner☆2,230Mar 18, 2025Updated last year
- Rapid Mapping-based Isoform Quantification from RNA-Seq Reads☆127Jun 9, 2022Updated 4 years ago
- Rapid sensitive and accurate read mapping via quasi-mapping☆90Jun 5, 2020Updated 6 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,410Jul 30, 2026Updated last week
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,484Aug 2, 2026Updated last week
- Useful tools for working with Salmon output☆38Jun 24, 2020Updated 6 years ago
- Transcript quantification import with automatic metadata detection☆72Jul 20, 2026Updated 3 weeks ago
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆475Updated this week
- Transcript assembly and quantification for RNA-Seq☆527Updated this week
- Graph-based alignment (Hierarchical Graph FM index)☆539Jul 31, 2026Updated last week
- SUPPA: Fast quantification of splicing and differential splicing☆306Nov 6, 2025Updated 9 months ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,230May 19, 2026Updated 2 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- The next version of bwa-mem☆858Oct 15, 2025Updated 9 months ago
- Trinity RNA-Seq de novo transcriptome assembly☆897Apr 23, 2026Updated 3 months ago
- Transcript quantification import for modular pipelines☆144Apr 15, 2026Updated 3 months ago
- Tools to process and analyze deep sequencing data.☆762Updated this week
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆493Jul 7, 2026Updated last month
- Cutadapt removes adapter sequences from sequencing reads☆586Jul 27, 2026Updated 2 weeks ago
- 🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transc…☆214Updated this week
- SRA Tools☆1,361Updated this week
- Prepare Sailfish and Salmon output for downstream analysis☆41Jun 6, 2019Updated 7 years ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- Tools for working with SAM/BAM data☆613Dec 22, 2024Updated last year
- Toolkit for processing sequences in FASTA/Q formats☆1,553Jun 1, 2025Updated last year
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆277Jul 7, 2026Updated last month
- Consistent adapter and quality trimming for NGS, with extra functionality for RRBS data☆571Updated this week
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,589Jul 8, 2026Updated last month
- BEDOPS: high-performance genomic feature operations☆375Apr 29, 2025Updated last year
- C++ API & command-line toolkit for working with BAM data☆431May 18, 2025Updated last year
- Tools for handling Unique Molecular Identifiers in NGS data sets☆549Jun 18, 2026Updated last month
- Fast fusion detection using kallisto☆80Jun 11, 2025Updated last year
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Tools for processing UMI RNA-tag data☆133Apr 30, 2026Updated 3 months ago
- An efficient index for the colored, compacted, de Bruijn graph☆112Jun 19, 2026Updated last month
- bedtools - the swiss army knife for genome arithmetic☆1,045Jun 10, 2026Updated 2 months ago
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,765Updated this week
- A fast and sensitive gapped read aligner☆809Jun 1, 2026Updated 2 months ago
- Scallop is a reference-based transcriptome assembler for RNA-seq☆95Apr 30, 2021Updated 5 years ago
- Accelerated BLAST compatible local sequence aligner.☆1,313Aug 4, 2026Updated last week