Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.

TitleSailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.
Publication TypeJournal Article
AuthorsPatro R, Mount SM, Kingsford C
2014
JournalNat Biotechnol
Volume32
Issue5
Pages462-4
algorithms, Brain Chemistry, Computational Biology, HUMANS, Models, Biological, RNA Isoforms, Sequence Analysis, RNA, software

We introduce Sailfish, a computational method for quantifying the abundance of previously annotated RNA isoforms from RNA-seq data. Because Sailfish entirely avoids mapping reads, a time-consuming step in all current methods, it provides quantification estimates much faster than do existing approaches (typically 20 times faster) without loss of accuracy. By facilitating frequent reanalysis of data and reducing the need to optimize parameters, Sailfish exemplifies the potential of lightweight algorithms for efficiently processing sequencing reads.

10.1038/nbt.2862
PubMed ID24752080
PubMed Central IDPMC4077321
Grant ListR01 HG007104 / HG / NHGRI NIH HHS / United States
R01HG007104 / HG / NHGRI NIH HHS / United States
R21 AI085376 / AI / NIAID NIH HHS / United States
R21 HG006913 / HG / NHGRI NIH HHS / United States
R21AI085376 / AI / NIAID NIH HHS / United States
R21HG006913 / HG / NHGRI NIH HHS / United States