Salmon provides fast and bias-aware quantification of transcript expression.
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ABSTRACT:
SUBMITTER: Patro R
PROVIDER: S-EPMC5600148 | biostudies-literature | 2017 Apr
REPOSITORIES: biostudies-literature
Publications
Salmon provides fast and bias-aware quantification of transcript expression.
Patro Rob R Duggal Geet G Love Michael I MI Irizarry Rafael A RA Kingsford Carl C
Nature methods 20170306 4
We introduce Salmon, a lightweight method for quantifying transcript abundance from RNA-seq reads. Salmon combines a new dual-phase parallel inference algorithm and feature-rich bias models with an ultra-fast read mapping procedure. It is the first transcriptome-wide quantifier to correct for fragment GC-content bias, which, as we demonstrate here, substantially improves the accuracy of abundance estimates and the sensitivity of subsequent differential expression analysis. ...[more]
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