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

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.

Pubmed ID: 22419786

Authors

  • Burriesci MS
  • Lehnert EM
  • Pringle JR

Journal

Bioinformatics (Oxford, England)

Publication Data

May 15, 2012

Associated Grants

  • Agency: NHGRI NIH HHS, Id: 5 T32 HG000044

Mesh Terms

  • Algorithms
  • Gene Expression Profiling
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Pseudomonas
  • Sequence Analysis, DNA
  • Software