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

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 approach...

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Main Authors:	Patro, Rob, Mount, Stephen M., Kingsford, Carl
Format:	Online
Language:	English
Published:	2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4077321/

id	pubmed-4077321
recordtype	oai_dc
spelling	pubmed-40773212014-11-01 Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms Patro, Rob Mount, Stephen M. Kingsford, Carl Article 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. 2014-04-20 2014-05 /pmc/articles/PMC4077321/ /pubmed/24752080 http://dx.doi.org/10.1038/nbt.2862 Text en http://www.nature.com/authors/editorial_policies/license.html#terms Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Patro, Rob Mount, Stephen M. Kingsford, Carl
spellingShingle	Patro, Rob Mount, Stephen M. Kingsford, Carl Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
author_facet	Patro, Rob Mount, Stephen M. Kingsford, Carl
author_sort	Patro, Rob
title	Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
title_short	Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
title_full	Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
title_fullStr	Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
title_full_unstemmed	Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
title_sort	sailfish enables alignment-free isoform quantification from rna-seq reads using lightweight algorithms
description	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.
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4077321/
_version_	1612108384506478592

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

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