kallisto paper summary: Near-optimal RNA-seq quantification




In case you missed it, kallisto, the new RNA-seq quantification method from Lior Pachter‘s group, was one of the biggest highlights from this year’s The Biology of the Genomes conference. kallisto team made the kallisto software immediately available and the preprint describing kallisto was available at arXiv pretty soon after the #BOG15. Near-optimal RNA-Seq quantification, Nicolas Bray, […]

RNA-Skim: new RNA-seq quantitation method that is faster than Sailfish




This is a quick post: summary/thoughts* on the new paper that got accepted at the upcoming ISMB 2014 and published in the special issue of  Bioinformatics. RNA-Skim: a rapid method for RNA-Seq quantification at transcript level  Zhaojun Zhang and Wei Wang is from a duo at UNC and UCLA. (*thoughts are always half baked :)) RNA-Skim is a […]

Sailfish: Alignment-free isoform quantification from RNA-seq reads




Sailfish – the fastest and alignmnet-free isoform-level quantitation of RNA-seq data is now published on Nature Biotechnology. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms, by Rob Patro,Stephen M Mount, & Carl Kingsford Sailfish manuscript was first available in the open preprint server arXiv in August 2013 and now it is in […]

Sailfish: Isoform Quantitation at the Speed of Making a Cup of Coffee




This is a really quick summary of the interesting paper “Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads using Lightweight Algorithms, by Rob Patro, Stephen M. Mount, Carl Kingsford” that was on arXiv and @Haldanesive early this week. Sailfish is a new computational approach that can quantify isoform level expression using RNA-seq data. What is novel about Sailfish […]