RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes.

ABSTRACT:

Motivation

The alignment of sequencing reads to a transcriptome is a common and important step in many RNA-seq analysis tasks. When aligning RNA-seq reads directly to a transcriptome (as is common in the de novo setting or when a trusted reference annotation is available), care must be taken to report the potentially large number of multi-mapping locations per read. This can pose a substantial computational burden for existing aligners, and can considerably slow downstream analysis.

Results

We introduce a novel concept, quasi-mapping, and an efficient algorithm implementing this approach for mapping sequencing reads to a transcriptome. By attempting only to report the potential loci of origin of a sequencing read, and not the base-to-base alignment by which it derives from t

SUBMITTER: Srivastava A 

PROVIDER: S-EPMC4908361 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature