Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.
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ABSTRACT:
SUBMITTER: Patro R
PROVIDER: S-EPMC4077321 | biostudies-literature | 2014 May
REPOSITORIES: biostudies-literature
Publications
Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.
Patro Rob R Mount Stephen M SM Kingsford Carl C
Nature biotechnology 20140420 5
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 alg ...[more]
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