Can I read FLASH: fast length adjustment of short reads to improve genome assemblies on EtoBox?

FLASH: fast length adjustment of short reads to improve genome assemblies by Tanja Magoč; Steven L. Salzberg is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

What is FLASH: fast length adjustment of short reads to improve genome assemblies about?

## Abstract Motivation: 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. Availabil

Who reads FLASH: fast length adjustment of short reads to improve genome assemblies?

Author

Tanja Magoč; Steven L. Salzberg

Publisher

Oxford University Press; Oxford University Press (OUP) (ISSN 1367-4803)

Published

2011

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)