Fulcrum: condensing redundant reads from high-throughput sequencing studies.

ABSTRACT:

Motivation

Ultra-high-throughput sequencing produces duplicate and near-duplicate reads, which can consume computational resources in downstream applications. A tool that collapses such reads should reduce storage and assembly complications and costs.

Results

We developed Fulcrum to collapse identical and near-identical Illumina and 454 reads (such as those from PCR clones) into single error-corrected sequences; it can process paired-end as well as single-end reads. Fulcrum is customizable and can be deployed on a single machine, a local network or a commercially available MapReduce cluster, and it has been optimized to maximize ease-of-use, cross-platform compatibility and future scalability. Sequence datasets have been collapsed by up to 71%, and the reduced number and imp

SUBMITTER: Burriesci MS 

PROVIDER: S-EPMC3348557 | biostudies-literature | 2012 May

REPOSITORIES: biostudies-literature