Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps

Genome Biol. 2010;11(4):R41. doi: 10.1186/gb-2010-11-4-r41. Epub 2010 Apr 13.


Advances in sequencing technology allow genomes to be sequenced at vastly decreased costs. However, the assembled data frequently are highly fragmented with many gaps. We present a practical approach that uses Illumina sequences to improve draft genome assemblies by aligning sequences against contig ends and performing local assemblies to produce gap-spanning contigs. The continuity of a draft genome can thus be substantially improved, often without the need to generate new data.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Base Sequence
  • Contig Mapping
  • Genomics / methods*
  • Sequence Analysis, DNA / methods*