title: Fulcrum: condensing redundant reads from high-throughput sequencing studies.
abstract: BACKGROUND
  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.
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA.
authors.forename: Matthew S
authors.initials: MS
authors.lastname: Burriesci
authors.forename: Erik M
authors.initials: EM
authors.lastname: Lehnert
authors.forename: John R
authors.initials: JR
authors.lastname: Pringle
mesh_terms: D000465:Algorithms; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D011549:Pseudomonas / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software