title: Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.
abstract: 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.
authors.affiliation: Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
authors.forename: Rob
authors.initials: R
authors.lastname: Patro
authors.affiliation: 1] Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA. [2] Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Mount
authors.affiliation: Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
authors.forename: Carl
authors.initials: C
authors.lastname: Kingsford
mesh_terms: D000465:Algorithms; D001923:Brain Chemistry; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D008954:Models, Biological; D059368:RNA Isoforms / Q000032:analysis / Q000737:chemistry / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D059368:RNA Isoforms
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