schliessen

Filtern

 

Bibliotheken

Near-optimal probabilistic RNA-seq quantification

We present kallisto, an RNA-seq quantification program that is two orders of magnitude faster than previous approaches and achieves similar accuracy. Kallisto pseudoaligns reads to a reference, producing a list of transcripts that are compatible with each read while avoiding alignment of individual... Full description

Journal Title: Nature biotechnology 2016-05, Vol.34 (5), p.525-527
Main Author: Bray, Nicolas L
Other Authors: Pimentel, Harold , Melsted, Páll , Pachter, Lior
Format: Electronic Article Electronic Article
Language: English
Subjects:
RNA
Publisher: United States: Nature Publishing Group
ID: ISSN: 1087-0156
Link: https://www.ncbi.nlm.nih.gov/pubmed/27043002
Zum Text:
SendSend as email Add to Book BagAdd to Book Bag
Staff View
recordid: cdi_proquest_miscellaneous_1790935059
title: Near-optimal probabilistic RNA-seq quantification
format: Article
creator:
  • Bray, Nicolas L
  • Pimentel, Harold
  • Melsted, Páll
  • Pachter, Lior
subjects:
  • Algorithms
  • Analysis
  • Biotechnology
  • Computer Simulation
  • Data Interpretation, Statistical
  • High-Throughput Nucleotide Sequencing - methods
  • Methods
  • Models, Statistical
  • Pattern Recognition, Automated - methods
  • Reproducibility of Results
  • Ribonucleic acid
  • RNA
  • RNA - genetics
  • RNA sequencing
  • Sensitivity and Specificity
  • Sequence Alignment - methods
  • Sequence Analysis, RNA - methods
  • Software
ispartof: Nature biotechnology, 2016-05, Vol.34 (5), p.525-527
description: We present kallisto, an RNA-seq quantification program that is two orders of magnitude faster than previous approaches and achieves similar accuracy. Kallisto pseudoaligns reads to a reference, producing a list of transcripts that are compatible with each read while avoiding alignment of individual bases. We use kallisto to analyze 30 million unaligned paired-end RNA-seq reads in
language: eng
source:
identifier: ISSN: 1087-0156
fulltext: no_fulltext
issn:
  • 1087-0156
  • 1546-1696
url: Link


@attributes
NO1
SEARCH_ENGINEprimo_central_multiple_fe
SEARCH_ENGINE_TYPEPrimo Central Search Engine
RANK2.893868
LOCALfalse
PrimoNMBib
record
control
sourceidgale_proqu
recordidTN_cdi_proquest_miscellaneous_1790935059
sourceformatXML
sourcesystemPC
galeidA454619622
sourcerecordidA454619622
originalsourceidFETCH-LOGICAL-1564t-4964d75d86ec3afea20539579bdc36821d67a291216fe6f4e8ece56583d9f7e00
addsrcrecordideNqNkl1LHDEUhoNUXKuCv6As9KaFzjbJ5GNyuYhfICtY29uQyZxsI7Mzu5MM1H9v9qOrq15IIAnhOe9J3rwInRI8IjgvfjZlHOWcqD10SDgTGRFKfEp7XMgMEy4G6HMIDxhjwYQ4QAMqMcsxpoeITMB0WTuPfmbq4bxrS1P62ofo7fBuMs4CLIaL3jTRO29N9G1zjPadqQOcbNYj9Pvi_P7sKru5vbw-G99kqR-LGVOCVZJXhQCbGweGYp4rLlVZ2VwUlFRCGqoIJcKBcAwKsMAFL_JKOQkYH6Fva910qUUPIeqZDxbq2jTQ9kETqbDKOebqA2ghmaSUL1W_vkIf2r5r0kNWFBWySOZsqampQfvGtbEzdimqxywZTJSgNFGjd6g0Kph52zbgfDrfKfi-U5CYCP_i1PQh6Otfdx9nb__ssj9esGUffAMhTcFP_8awLtnBN3bZrg2hA6fnXfr-7lETrJd50ilPepmnhH7Z2NWXM6i24P8APXuw1bI-rnKSvPD1W8UnDVHOyg
sourcetypeAggregation Database
isCDItrue
recordtypearticle
pqid1787267827
display
typearticle
titleNear-optimal probabilistic RNA-seq quantification
creatorBray, Nicolas L ; Pimentel, Harold ; Melsted, Páll ; Pachter, Lior
creatorcontribBray, Nicolas L ; Pimentel, Harold ; Melsted, Páll ; Pachter, Lior
descriptionWe present kallisto, an RNA-seq quantification program that is two orders of magnitude faster than previous approaches and achieves similar accuracy. Kallisto pseudoaligns reads to a reference, producing a list of transcripts that are compatible with each read while avoiding alignment of individual bases. We use kallisto to analyze 30 million unaligned paired-end RNA-seq reads in <10 min on a standard laptop computer. This removes a major computational bottleneck in RNA-seq analysis.
identifier
0ISSN: 1087-0156
1EISSN: 1546-1696
2DOI: 10.1038/nbt.3519
3PMID: 27043002
languageeng
publisherUnited States: Nature Publishing Group
subjectAlgorithms ; Analysis ; Biotechnology ; Computer Simulation ; Data Interpretation, Statistical ; High-Throughput Nucleotide Sequencing - methods ; Methods ; Models, Statistical ; Pattern Recognition, Automated - methods ; Reproducibility of Results ; Ribonucleic acid ; RNA ; RNA - genetics ; RNA sequencing ; Sensitivity and Specificity ; Sequence Alignment - methods ; Sequence Analysis, RNA - methods ; Software
ispartofNature biotechnology, 2016-05, Vol.34 (5), p.525-527
rights
0COPYRIGHT 2016 Nature Publishing Group
1Copyright Nature Publishing Group May 2016
lds50peer_reviewed
citedbyFETCH-LOGICAL-1564t-4964d75d86ec3afea20539579bdc36821d67a291216fe6f4e8ece56583d9f7e00
citesFETCH-LOGICAL-1564t-4964d75d86ec3afea20539579bdc36821d67a291216fe6f4e8ece56583d9f7e00
orcidid0000-0002-8418-6724
links
openurl$$Topenurl_article
thumbnail$$Usyndetics_thumb_exl
backlink$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27043002$$D View this record in MEDLINE/PubMed
search
creatorcontrib
0Bray, Nicolas L
1Pimentel, Harold
2Melsted, Páll
3Pachter, Lior
title
0Near-optimal probabilistic RNA-seq quantification
1Nature biotechnology
addtitleNat Biotechnol
descriptionWe present kallisto, an RNA-seq quantification program that is two orders of magnitude faster than previous approaches and achieves similar accuracy. Kallisto pseudoaligns reads to a reference, producing a list of transcripts that are compatible with each read while avoiding alignment of individual bases. We use kallisto to analyze 30 million unaligned paired-end RNA-seq reads in <10 min on a standard laptop computer. This removes a major computational bottleneck in RNA-seq analysis.
subject
0Algorithms
1Analysis
2Biotechnology
3Computer Simulation
4Data Interpretation, Statistical
5High-Throughput Nucleotide Sequencing - methods
6Methods
7Models, Statistical
8Pattern Recognition, Automated - methods
9Reproducibility of Results
10Ribonucleic acid
11RNA
12RNA - genetics
13RNA sequencing
14Sensitivity and Specificity
15Sequence Alignment - methods
16Sequence Analysis, RNA - methods
17Software
issn
01087-0156
11546-1696
fulltextfalse
rsrctypearticle
creationdate2016
recordtypearticle
recordideNqNkl1LHDEUhoNUXKuCv6As9KaFzjbJ5GNyuYhfICtY29uQyZxsI7Mzu5MM1H9v9qOrq15IIAnhOe9J3rwInRI8IjgvfjZlHOWcqD10SDgTGRFKfEp7XMgMEy4G6HMIDxhjwYQ4QAMqMcsxpoeITMB0WTuPfmbq4bxrS1P62ofo7fBuMs4CLIaL3jTRO29N9G1zjPadqQOcbNYj9Pvi_P7sKru5vbw-G99kqR-LGVOCVZJXhQCbGweGYp4rLlVZ2VwUlFRCGqoIJcKBcAwKsMAFL_JKOQkYH6Fva910qUUPIeqZDxbq2jTQ9kETqbDKOebqA2ghmaSUL1W_vkIf2r5r0kNWFBWySOZsqampQfvGtbEzdimqxywZTJSgNFGjd6g0Kph52zbgfDrfKfi-U5CYCP_i1PQh6Otfdx9nb__ssj9esGUffAMhTcFP_8awLtnBN3bZrg2hA6fnXfr-7lETrJd50ilPepmnhH7Z2NWXM6i24P8APXuw1bI-rnKSvPD1W8UnDVHOyg
startdate201605
enddate201605
creator
0Bray, Nicolas L
1Pimentel, Harold
2Melsted, Páll
3Pachter, Lior
generalNature Publishing Group
scope
0CGR
1CUY
2CVF
3ECM
4EIF
5NPM
6AAYXX
7CITATION
83V.
97QO
107QP
117QR
127T7
137TK
147TM
157X7
167XB
1788A
1888E
1988I
208AO
218FD
228FE
238FG
248FH
258FI
268FJ
278FK
288G5
29ABJCF
30ABUWG
31AZQEC
32BBNVY
33BENPR
34BGLVJ
35BHPHI
36C1K
37DWQXO
38FR3
39FYUFA
40GHDGH
41GNUQQ
42GUQSH
43HCIFZ
44K9.
45L6V
46LK8
47M0S
48M1P
49M2O
50M2P
51M7P
52M7S
53MBDVC
54P64
55PADUT
56PQEST
57PQQKQ
58PQUKI
59PRINS
60PTHSS
61Q9U
62RC3
637X8
orcididhttps://orcid.org/0000-0002-8418-6724
sort
creationdate201605
titleNear-optimal probabilistic RNA-seq quantification
authorBray, Nicolas L ; Pimentel, Harold ; Melsted, Páll ; Pachter, Lior
facets
frbrtype5
frbrgroupidcdi_FETCH-LOGICAL-1564t-4964d75d86ec3afea20539579bdc36821d67a291216fe6f4e8ece56583d9f7e00
rsrctypearticles
prefilterarticles
languageeng
creationdate2016
topic
0Algorithms
1Analysis
2Biotechnology
3Computer Simulation
4Data Interpretation, Statistical
5High-Throughput Nucleotide Sequencing - methods
6Methods
7Models, Statistical
8Pattern Recognition, Automated - methods
9Reproducibility of Results
10Ribonucleic acid
11RNA
12RNA - genetics
13RNA sequencing
14Sensitivity and Specificity
15Sequence Alignment - methods
16Sequence Analysis, RNA - methods
17Software
toplevelpeer_reviewed
creatorcontrib
0Bray, Nicolas L
1Pimentel, Harold
2Melsted, Páll
3Pachter, Lior
collection
0Medline
1MEDLINE
2MEDLINE (Ovid)
3MEDLINE
4MEDLINE
5PubMed
6CrossRef
7ProQuest Central (Corporate)
8Biotechnology Research Abstracts
9Calcium & Calcified Tissue Abstracts
10Chemoreception Abstracts
11Industrial and Applied Microbiology Abstracts (Microbiology A)
12Neurosciences Abstracts
13Nucleic Acids Abstracts
14Health & Medical Collection
15ProQuest Central (purchase pre-March 2016)
16Biology Database (Alumni Edition)
17Medical Database (Alumni Edition)
18Science Database (Alumni Edition)
19ProQuest Pharma Collection
20Technology Research Database
21ProQuest SciTech Collection
22ProQuest Technology Collection
23ProQuest Natural Science Collection
24Hospital Premium Collection
25Hospital Premium Collection (Alumni Edition)
26ProQuest Central (Alumni) (purchase pre-March 2016)
27Research Library (Alumni Edition)
28Materials Science & Engineering Collection
29ProQuest Central (Alumni Edition)
30ProQuest Central Essentials
31Biological Science Collection
32ProQuest Central
33Technology Collection
34Natural Science Collection
35Environmental Sciences and Pollution Management
36ProQuest Central Korea
37Engineering Research Database
38Health Research Premium Collection
39Health Research Premium Collection (Alumni)
40ProQuest Central Student
41Research Library Prep
42SciTech Premium Collection
43ProQuest Health & Medical Complete (Alumni)
44ProQuest Engineering Collection
45ProQuest Biological Science Collection
46Health & Medical Collection (Alumni Edition)
47Medical Database
48Research Library
49Science Database
50Biological Science Database
51Engineering Database
52Research Library (Corporate)
53Biotechnology and BioEngineering Abstracts
54Research Library China
55ProQuest One Academic Eastern Edition
56ProQuest One Academic
57ProQuest One Academic UKI Edition
58ProQuest Central China
59Engineering Collection
60ProQuest Central Basic
61Genetics Abstracts
62MEDLINE - Academic
jtitleNature biotechnology
delivery
delcategoryRemote Search Resource
fulltextno_fulltext
addata
au
0Bray, Nicolas L
1Pimentel, Harold
2Melsted, Páll
3Pachter, Lior
formatjournal
genrearticle
ristypeJOUR
atitleNear-optimal probabilistic RNA-seq quantification
jtitleNature biotechnology
addtitleNat Biotechnol
date2016-05
risdate2016
volume34
issue5
spage525
epage527
pages525-527
issn1087-0156
eissn1546-1696
abstractWe present kallisto, an RNA-seq quantification program that is two orders of magnitude faster than previous approaches and achieves similar accuracy. Kallisto pseudoaligns reads to a reference, producing a list of transcripts that are compatible with each read while avoiding alignment of individual bases. We use kallisto to analyze 30 million unaligned paired-end RNA-seq reads in <10 min on a standard laptop computer. This removes a major computational bottleneck in RNA-seq analysis.
copUnited States
pubNature Publishing Group
pmid27043002
doi10.1038/nbt.3519
tpages4
orcididhttps://orcid.org/0000-0002-8418-6724