FLASH

FLASH is a computational tool designed to merge overlapping paired-end reads from fragment libraries, which can extend short reads and improve genome assembly. FLASH was tested on simulated read pairs and applied to genome assemblies of bacteria and human chromosomes with high accuracy (>99% correct extension and merging). The resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds.

Topic

Sequencing;Sequence assembly;Bioinformatics

Detail

  • Operation: Read pre-processing;Sequence merging;Sequence assembly

  • Software interface: Command-line user interface

  • Language: C

  • License: -

  • Cost: Free

  • Version name: 1.2.11

  • Credit: National Institutes of Health.

  • Input: -

  • Output: -

  • Contact: flash.comment@gmail.com.

  • Collection: -

  • Maturity: -

Publications

  • FLASH: fast length adjustment of short reads to improve genome assemblies.
  • Magoč T and Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. FLASH: fast length adjustment of short reads to improve genome assemblies. 2011; 27:2957-63. doi: 10.1093/bioinformatics/btr507
  • https://doi.org/10.1093/bioinformatics/btr507
  • PMID: 21903629
  • PMC: PMC3198573

Download and documentation

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