🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
☆862May 29, 2024Updated last year
Alternatives and similar repositories for salmon
Users that are interested in salmon are comparing it to the libraries listed below
Sorting:
- Near-optimal RNA-Seq quantification☆724Jan 20, 2026Updated last month
- Differential analysis of RNA-Seq☆312May 28, 2025Updated 9 months ago
- Rapid Mapping-based Isoform Quantification from RNA-Seq Reads☆127Jun 9, 2022Updated 3 years ago
- RNA-seq aligner☆2,146Mar 18, 2025Updated 11 months ago
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,292Jan 22, 2026Updated last month
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,425Updated this week
- Rapid sensitive and accurate read mapping via quasi-mapping☆90Jun 5, 2020Updated 5 years ago
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆461Updated this week
- Transcript assembly and quantification for RNA-Seq☆489Dec 26, 2025Updated 2 months ago
- Graph-based alignment (Hierarchical Graph FM index)☆530Jan 27, 2026Updated last month
- Transcript quantification import with automatic metadata detection☆69Feb 3, 2026Updated 3 weeks ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,128Feb 13, 2026Updated 2 weeks ago
- The next version of bwa-mem☆819Oct 15, 2025Updated 4 months ago
- Tools to process and analyze deep sequencing data.☆751Jul 23, 2025Updated 7 months ago
- Trinity RNA-Seq de novo transcriptome assembly☆883Feb 7, 2025Updated last year
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆462Dec 26, 2024Updated last year
- SUPPA: Fast quantification of splicing and differential splicing☆293Nov 6, 2025Updated 3 months ago
- Useful tools for working with Salmon output☆39Jun 24, 2020Updated 5 years ago
- Cutadapt removes adapter sequences from sequencing reads☆572Jan 12, 2026Updated last month
- SRA Tools☆1,309Updated this week
- Toolkit for processing sequences in FASTA/Q formats☆1,528Jun 1, 2025Updated 9 months ago
- Tools for working with SAM/BAM data☆605Dec 22, 2024Updated last year
- Tools for processing UMI RNA-tag data☆131Mar 15, 2023Updated 2 years ago
- Transcript quantification import for modular pipelines☆142Sep 30, 2025Updated 5 months ago
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆262Jul 12, 2025Updated 7 months ago
- 🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transc…☆201Jan 27, 2026Updated last month
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,520Updated this week
- C++ API & command-line toolkit for working with BAM data☆429May 18, 2025Updated 9 months ago
- Tools for handling Unique Molecular Identifiers in NGS data sets☆537Feb 2, 2026Updated last month
- BEDOPS: high-performance genomic feature operations☆360Apr 29, 2025Updated 10 months ago
- A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…☆541Updated this week
- bedtools - the swiss army knife for genome arithmetic☆1,025Mar 11, 2025Updated 11 months ago
- Fast fusion detection using kallisto☆79Jun 11, 2025Updated 8 months ago
- R toolkit for single cell genomics☆2,661Feb 20, 2026Updated last week
- 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
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,707Mar 22, 2025Updated 11 months ago
- Accelerated BLAST compatible local sequence aligner.☆1,245Feb 23, 2026Updated last week
- GFF and GTF file manipulation and interconversion☆314Jan 26, 2026Updated last month
- RNAseq analysis notes from Ming Tang☆1,069Nov 15, 2021Updated 4 years ago