Fragment assignment in the cloud with eXpress-D.

ABSTRACT:

Background

Probabilistic assignment of ambiguously mapped fragments produced by high-throughput sequencing experiments has been demonstrated to greatly improve accuracy in the analysis of RNA-Seq and ChIP-Seq, and is an essential step in many other sequence census experiments. A maximum likelihood method using the expectation-maximization (EM) algorithm for optimization is commonly used to solve this problem. However, batch EM-based approaches do not scale well with the size of sequencing datasets, which have been increasing dramatically over the past few years. Thus, current approaches to fragment assignment rely on heuristics or approximations for tractability.

Results

We present an implementation of a distributed EM solution to the fragment assignment problem using Spark,

SUBMITTER: Roberts A 

PROVIDER: S-EPMC3881492 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature