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, […]

Kallisto, a new ultra fast RNA-seq quantitation method

[Update:] Since the post was published, a preprint on Kallisto manuscript is available. Lior Pachter has writtena blog post on pseudo-aligments and Rob Patro has a nice post on “Light weight algorithms for RNA-seq”. Here there. kallisto preprint Near-optimal RNA-Seq quantification with kallisto Rob Patro’s blog post: Not-quite alignments: Salmon, kallisto and efficient quantification of […]

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 […]

ISMB 2014 Accepted Papers List

ISMB 2014, one of the largest Bioinformatics/Computational Biology conferences, to he held in Boston this year from July 11 – 15, 2014 announced the list of papers accepted for conference proceedings. The accepted papers will be presented as talks in the conference and published as conference proceedings in a special issue of Bioinformatics journal online. […]

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 […]