Journal
NATURE BIOTECHNOLOGY
Volume 32, Issue 5, Pages 462-U174Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/nbt.2862
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Funding
- US National Science Foundation [CCF-1256087, CCF-1053918, EF-0849899]
- US National Institutes of Health [R21AI085376, R21HG006913, R01HG007104]
- Direct For Computer & Info Scie & Enginr
- Division of Computing and Communication Foundations [1319998] Funding Source: National Science Foundation
- Division of Computing and Communication Foundations
- Direct For Computer & Info Scie & Enginr [1256087] Funding Source: National Science Foundation
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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.
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