Home LiteratureArticle Details
PMID: 24752080 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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

Nature biotechnology ·Vol. 32 ·No. 5 ·2014-05-00 ·Pages 462-4

Patro R, Mount SM, Kingsford C

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.

MeSH Terms
Algorithms Brain Chemistry Computational Biology/methods Humans Models, Biological RNA Isoforms/analysis,chemistry,genetics Sequence Analysis, RNA/methods Software
Chemicals
RNA Isoforms
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Patro Rob
Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
Mount Stephen M
1] Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA. [2] Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.
Kingsford Carl
Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
References (20)
20 references, click to expand
  1. CRAC: an integrated approach to the analysis of RNA-seq reads.
    Genome Biol. 2013 Mar 28;14(3):R30 PMID: 23537109
  2. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D130-5 PMID: 22121212
  3. TopHat: discovering splice junctions with RNA-Seq.
    Bioinformatics. 2009 May 1;25(9):1105-11 PMID: 19289445
  4. A comparison of methods for differential expression analysis of RNA-seq data.
    BMC Bioinformatics. 2013 Mar 09;14:91 PMID: 23497356
  5. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.
    Bioinformatics. 2011 Mar 15;27(6):764-70 PMID: 21217122
  6. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
    Genome Biol. 2009;10(3):R25 PMID: 19261174
  7. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
    Nat Biotechnol. 2010 May;28(5):511-5 PMID: 20436464
  8. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments.
    BMC Bioinformatics. 2010 Feb 18;11:94 PMID: 20167110
  9. Full-length transcriptome assembly from RNA-Seq data without a reference genome.
    Nat Biotechnol. 2011 May 15;29(7):644-52 PMID: 21572440
  10. Estimation of alternative splicing isoform frequencies from RNA-Seq data.
    Algorithms Mol Biol. 2011 Apr 19;6(1):9 PMID: 21504602
  11. KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.
    BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S5 PMID: 22537044
  12. Ensembl 2013.
    Nucleic Acids Res. 2013 Jan;41(Database issue):D48-55 PMID: 23203987
  13. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.
    BMC Bioinformatics. 2011 Aug 04;12:323 PMID: 21816040
  14. Mapping and quantifying mammalian transcriptomes by RNA-Seq.
    Nat Methods. 2008 Jul;5(7):621-8 PMID: 18516045
  15. Personalized oncology through integrative high-throughput sequencing: a pilot study.
    Sci Transl Med. 2011 Nov 30;3(111):111ra121 PMID: 22133722
  16. Modelling and simulating generic RNA-Seq experiments with the flux simulator.
    Nucleic Acids Res. 2012 Nov 1;40(20):10073-83 PMID: 22962361
  17. Streaming fragment assignment for real-time analysis of sequencing experiments.
    Nat Methods. 2013 Jan;10(1):71-3 PMID: 23160280
  18. Statistical Modeling of RNA-Seq Data.
    Stat Sci. 2011 Feb;26(1): PMID: 24307754
  19. Bias detection and correction in RNA-Sequencing data.
    BMC Bioinformatics. 2011 Jul 19;12:290 PMID: 21771300
  20. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.
    Nat Biotechnol. 2006 Sep;24(9):1151-61 PMID: 16964229
Article Info
Journal
Nature biotechnology
Abbr.
Nat Biotechnol
ISSN
1546-1696
DOI
10.1038/nbt.2862
Published
2014-05-00
Epub
2014-00-20
Pages
462-4
Language
English
Region
United States
NLM ID
9604648
PMCID
PMC4077321
Subset
IM
Grants
NIAID NIH HHS · R21 AI085376 · United States
NHGRI NIH HHS · R01 HG007104 · United States
NHGRI NIH HHS · R21 HG006913 · United States
NHGRI NIH HHS · R01HG007104 · United States
NIAID NIH HHS · R21AI085376 · United States
NHGRI NIH HHS · R21HG006913 · United States
External Links
PubMed source DOI: 10.1038/nbt.2862 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2