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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:
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
Publisher: United States: Nature Publishing Group
ID: ISSN: 1087-0156
Link: https://www.ncbi.nlm.nih.gov/pubmed/27043002
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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


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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.
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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.
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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.
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