Introduction

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.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.

Publications

  1. Fulcrum: condensing redundant reads from high-throughput sequencing studies.
    Cite this
    Burriesci MS, Lehnert EM, Pringle JR, 2012-05-01 - Bioinformatics (Oxford, England)

Credits

  1. Matthew S Burriesci
    Developer

    Department of Genetics, Stanford University School of Medicine, United States of America

  2. Erik M Lehnert
    Developer

  3. John R Pringle
    Investigator

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Summary
AccessionBT000439
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByJohn R Pringle