Introducing a New Collection of Open-source Salmon Features! 

Over the last year Ocean Genomics has, with the help of a grant from the Chan Zuckerberg Initiative, developed several new features and applications for the open-source Salmon application and ecosystem. These features include enhancements to single cell analysis, ONT Long Reads, Soft Clipping support, and additional BAM format support. For full details, and documentation, see below: 

Single Cell Enhancements: 

  • SciSeq – Use salmon and alevin-fry to process 3-level single cell combinatorial indexing RNA sequencing (sci-RNA-seq3) reads. View Tutorial 
  • SPLiT-Seq – Analyze SPLiT-pool ligation-based transcriptome sequencing (SPLiT-seq) reads using Alevin-fry. View Tutorial 
  • Custom Protocols – Salmon and alevin-fry now support most single-cell RNA-seq protocols using the custom geometry flag. COMING SOON! 

NEW Quantification from Genomic Alignments Support: Mudskipper, a new addition to the Salmon ecosystem that converts genomic alignments in BAM/SAM formats to transcriptomic alignments in BAM format or RAD format. This is done by projecting alignment coordinates based on the transcript annotations passed as input in GTF format. Mudskipper is available on Github, Bioconda and Cargo. View Tutorials 

Soft Clipping and Accurate CIGAR: With Salmon’s new soft-clipping functionality, you con align read sequences to short targets or remove extraneous adapters with high precision to achieve more accurate transcript quantification results. COMING SOON! 

ONT Long Read Support: Use Salmon to quantify Oxford Nanopore Technologies (ONT) long-reads (both cDNA and direct RNA) which now has an enhanced alignment error model specially designed to work with long-reads. View Tutorial

 For more information, documentation, tutorials or to download the latest version of Salmon visit