title: FLASH: fast length adjustment of short reads to improve genome assemblies.
abstract: BACKGROUND
  Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome.
  
  
  RESULTS
  We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds.
  
  
  METHODS
  The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash.
  
  
  BACKGROUND
  t.magoc@gmail.com.
authors: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. t.magoc@gmail.com
authors: Tanja
authors: T
authors: Magoč
authors: Steven L
authors: SL
authors: Salzberg
mesh_terms: D002883:Chromosomes, Human, Pair 14; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D017422:Sequence Analysis, DNA; D012984:Software; D013211:Staphylococcus aureus / Q000235:genetics