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Bioinformatics. 2012 May 15;28(10):1324-7. doi: 10.1093/bioinformatics/bts123. Epub 2012 Mar 13.

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

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  • 1Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA.

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 improved quality of the resulting sequences allow assemblers to produce longer contigs while using less memory.

PMID:
22419786
PMCID:
PMC3348557
DOI:
10.1093/bioinformatics/bts123
[PubMed - indexed for MEDLINE]
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