Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing.

ABSTRACT:

Background

Paired-tag sequencing approaches are commonly used for the analysis of genome structure. However, mammalian genomes have a complex organization with a variety of repetitive elements that complicate comprehensive genome-wide analyses.

Results

Here, we systematically assessed the utility of paired-end and mate-pair (MP) next-generation sequencing libraries with insert sizes ranging from 170 bp to 25 kb, for genome coverage and for improving scaffolding of a mammalian genome (Rattus norvegicus). Despite a lower library complexity, large insert MP libraries (20 or 25 kb) provided very high physical genome coverage and were found to efficiently span repeat elements in the genome. Medium-sized (5, 8 or 15 kb) MP libraries were much more efficient for genome structure an

SUBMITTER: van Heesch S 

PROVIDER: S-EPMC3648348 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature