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

A new algorithm speeds up the quantification of transcripts from RNA-seq data by doing away with read mapping. 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-co...

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Bibliographic Details
Published in:Nature biotechnology 2014-05, Vol.32 (5), p.462-464
Main Authors: Patro, Rob, Mount, Stephen M, Kingsford, Carl
Format: Article
Language:English
Subjects:
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38/91
45/91
631/114/2785
631/114/794
631/1647/514/1949
631/61/212/2019
Agriculture
Algorithms
Bioinformatics
Biomedical Engineering/Biotechnology
Biomedicine
Biotechnology
Brain Chemistry
brief-communication
Computational Biology - methods
Genetic research
Humans
Life Sciences
Methods
Models, Biological
Ribonucleic acid
RNA
RNA Isoforms - analysis
RNA Isoforms - chemistry
RNA Isoforms - genetics
RNA sequencing
Sequence Analysis, RNA - methods
Software
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Summary:A new algorithm speeds up the quantification of transcripts from RNA-seq data by doing away with read mapping. 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.
ISSN:1087-0156
1546-1696
DOI:10.1038/nbt.2862