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- Title
Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.
- Authors
Patro, Rob; Mount, Stephen M; Kingsford, Carl
- 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.
- Subjects
RNA sequencing; SAILFISH; SEQUENCE (Linguistics); INDEXING; PREDICATE calculus
- Publication
Nature Biotechnology, 2014, Vol 32, Issue 5, p462
- ISSN
1087-0156
- Publication type
Article
- DOI
10.1038/nbt.2862