De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer

Abstract

Novel high-throughput DNA sequencing technologies allow researchers to characterize a bacterial genome during a single experiment and at a moderate cost. However, the increase in sequencing throughput that is allowed by using such platforms is obtained at the expense of individual sequence read length, which must be assembled into longer contigs to be exploitable. This study focuses on the Illumina sequencing platform that produces millions of very short sequences that are 35 bases in length. We propose a de novo assembler software that is dedicated to process such data. Based on a classical overlap graph representation and on the detection of potentially spurious reads, our software generates a set of accurate contigs of several kilobases that cover most of the bacterial genome. The assembly results were validated by comparing data sets that were obtained experimentally for Staphylococcus aureus strain MW2 and Helicobacter acinonychis strain Sheeba with that of their published genomes acquired by conventional sequencing of 1.5-to 3.0-kb fragments. We also provide indications that the broad coverage achieved by high-throughput sequencing might allow for the detection of clonal polymorphisms in the set of DNA molecules being sequenced.

Evaluation of next-generation sequencing software in mapping and assembly

“…It provides better and more preferable performance in terms of speed and output quality 44 compared with the other tools mentioned above. The second category of software that includes CABOG, 45 Edena, 46 Newbler 47 and Shorty 48 are based on overlap-layout-consensus. This strategy involves three main steps.…”

ABySS: A parallel assembler for short read sequence data

“…SRX000429). We performed assemblies with ABySS, Velvet (Zerbino and Birney 2008), EULER-SR (Chaisson and Pevzner 2008), SSAKE (Warren et al 2007), and Edena (Hernandez et al 2008). All assemblers were run in pairedend mode with the exception of Edena, which does not support the use of paired-end information in contig construction.…”

“…This paradigm was also followed in the VCAKE algorithm by Jeck et al (2007), and in the SHARCGS algorithm by Dohm et al (2007). On a third branch, Edena (Hernandez et al 2008) was an adaptation of the traditional overlap-layout-consensus model to short reads. These short read de novo assemblers are single-threaded applications designed to run on a single processor.…”

Next‐generation sequencing approaches in genetic rodent model systems to study functional effects of human genetic variation

“…Many organisms have unique features, but lack the genomic characterization that stems from advances such as genome assembly. Last year, the feasibility of de novo genome assembly using short reads was demonstrated for bacterial genomes [26,27] and we can expect that de novo assemblies of more complex genomes will follow. While good reference genomes are available for both mouse and rat, resequencing additional strains will require some degree of de novo assembly as well, as genomic segments that are lacking in a reference genome are not automatically included in de novo assemblies based on short read-based shotgun resequencing.…”