Alignment-Free Rapid Sequence Census Quantification (Kallisto)
- Technology Benefits
- Hundreds of times faster than standard tools (can quantify 30 million human reads in less than 3 minutes) Increased accuracy, especially compared to programs that shred reads into k-mersTractable to use the bootstrap to determine uncertainty on estimates and includes infrastructure for managing the large amount of data associated with bootstrapped samples
- Technology Application
- RNA-Seq analysis and quantificationSequence census experiments for copy number variation analysis of DNA sequencingHigh-throughput sequencing
- Detailed Technology Description
- None
- Others
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Tech ID/UC Case
25009/2015-156-0
Related Cases
2015-156-0, 2015-121-0
- *Abstract
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Sequence census experiments utilize next-generation sequence data to estimate the relative abundance of target sequences. Since the samples are often short DNA fragments, they must first be assigned to the correct transcripts and genes that produced them, and this alignment or mapping step currently takes up the majority of computing power and time in most expression analyses.
To avoid this costly process, UC Berkeley researchers have developed a software program (kallisto) for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads based on pseudo-alignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Pseudo-alignment of reads preserves the key information needed for quantification.
- *Applications
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- *Principal Investigator
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Name: Nicholas Bray
Department:
Name: Páll Melsted
Department:
Name: Lior Pachter
Department:
Name: Harold Pimentel
Department:
- Country/Region
- USA
