assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies评估使用mate-pairs解决重复的好处在新创短内容原核的组件.pdfVIP

Wetzel et al. BMC Bioinformatics 2011, 12:95 /1471-2105/12/95 RESEARCH ARTICLE Open Access Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies 1 2 2* Joshua Wetzel , Carl Kingsford and Mihai Pop Abstract Background: Next-generation sequencing technologies allow genomes to be sequenced more quickly and less expensively than ever before. However, as sequencing technology has improved, the difficulty of de novo genome assembly has increased, due in large part to the shorter reads generated by the new technologies. The use of mated sequences (referred to as mate-pairs) is a standard means of disambiguating assemblies to obtain a more complete picture of the genome without resorting to manual finishing. Here, we examine the effectiveness of mate-pair information in resolving repeated sequences in the DNA (a paramount issue to overcome). While it has been empirically accepted that mate-pairs improve assemblies, and a variety of assemblers use mate-pairs in the context of repeat resolution, the effectiveness of mate-pairs in this context has not been systematically evaluated in previous literature. Results: We show that, in high-coverage prokaryotic assemblies, libraries of short mate-pairs (about 4-6 times the read-length) more effectively disambiguate repeat regions than the libraries that are commonly constructed in current genome projects. We also demonstrate that the best assemblies can be obtained by ‘tuning’ mate-pair libraries to accommodate the specific repeat structure of the genome being assembled - information that can be obtained through an initial assembly using unpaired reads. These results are shown across 360 simulations on ‘ideal’ prokaryotic data as well as assembly of 8 bacterial g