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Nat Biotechnol. 2014 May;32(5):462-4. doi: 10.1038/nbt.2862. Epub 2014 Apr 20.

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

Author information

1
Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
2
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.

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.

PMID:
24752080
PMCID:
PMC4077321
DOI:
10.1038/nbt.2862
[Indexed for MEDLINE]
Free PMC Article

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