Near-optimal probabilistic RNA-seq quantification
Abstract
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 <10 min on a standard laptop computer. This removes a major computational bottleneck in RNA-seq analysis.
Additional Information
© 2016 Springer Nature Publishing AG. Received 15 October 2015; Accepted 25 February 2016; Published 04 April 2016. N.L.B., H.P. and L.P. were partially funded by NIH R01 HG006129. P.M. was partially funded by a Fulbright fellowship. Author Contributions: N.L.B. and L.P. developed the concept of pseudoalignment and conceived the idea for applying it to RNA-seq quantification. P.M. conceived the implementation using De Bruijn graphs. N.L.B., H.P., P.M. and L.P. designed the kallisto software and N.L.B. implemented a prototype. H.P. and P.M. wrote the current kallisto implementation. N.B. and H.P. automated production of the results. N.L.B., H.P., P.M. and L.P. analyzed results and wrote the paper. The authors declare no competing financial interests.Errata
In the version of this article initially published, in the HTML version only, the equation "α_tN > 0.01" was written as "α_(tN) > 0.01." In addition, in the Figure 1 legend, the formatting of the nodes was incorrect (v_1, etc., rather than v1). The errors have been corrected in the HTML and PDF versions of the article.Attached Files
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Additional details
- Eprint ID
- 95246
- Resolver ID
- CaltechAUTHORS:20190506-110012992
- R01 HG006129
- NIH
- Fulbright Foundation
- Created
-
2019-05-06Created from EPrint's datestamp field
- Updated
-
2023-06-01Created from EPrint's last_modified field