Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).

ABSTRACT:

Motivation

A critical task in high-throughput sequencing is aligning millions of short reads to a reference genome. Alignment is especially complicated for RNA sequencing (RNA-Seq) because of RNA splicing. A number of RNA-Seq algorithms are available, and claim to align reads with high accuracy and efficiency while detecting splice junctions. RNA-Seq data are discrete in nature; therefore, with reasonable gene models and comparative metrics RNA-Seq data can be simulated to sufficient accuracy to enable meaningful benchmarking of alignment algorithms. The exercise to rigorously compare all viable published RNA-Seq algorithms has not been performed previously.

Results

We developed an RNA-Seq simulator that models the main impediments to RNA alignment, including alternative spl

SUBMITTER: Grant GR 

PROVIDER: S-EPMC3167048 | biostudies-literature | 2011 Sep

REPOSITORIES: biostudies-literature