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

By David Hernández, Patrice François, Laurent Farinelli, M. Osteras, Jacques Schrenzel. Genome Research, 2008

659 citations recorded by the source corpus.

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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/247155e4869268787520dfc912d597bd4191c608

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Citations in the corpus

Optimization of de novo transcriptome assembly from next-generation sequencing data. (2010, methodology): “Current assemblers using this graph-based approach include ALLPATHS (Butler et al. 2008) and ALLPATHS 2 (MacCallum et al. 2009), Edena (Hernandez et al. 2008), Velvet (Zerbino and Birney 2008), EULER-SR (Chaisson and Pevzner 2008), and ABySS (Simpson et al. 2009).”
Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies (2010, background): “The homopolymer problem arises because the intensity of emitted light is linear when the number of incorporated nucleotides in the homopolymeric region is low, but is not linear when too many nucleotides are incorporated at once.”
ABySS: a parallel assembler for short read sequence data. (2009, methodology): “On a third branch, Edena (Hernandez et al. 2008) was an”
De novo assembly of human genomes with massively parallel short read sequencing. (2010, methodology): “…size of E. coli library (SRX000429); the other assemblers, including ABySS (Simpson et al. 2009), Velvet (Zerbino and Birney 2008), EULER-SR (Chaisson and Pevzner 2008), SSAKE (Warren et al. 2007), and Edena (Hernandez et al. 2008), have been evaluated using this data set (Simpson et al. 2009).”
IDBA - A Practical Iterative de Bruijn Graph De Novo Assembler (2010, methodology): “Our observations are confirmed by the N50 comparison of Edena [9] (currently one of the best string graph algorithms), Velvet [7] and Abyss [8] (the best de Bruijn graph algorithms) based on different coverage and error r ates of the data as shown in Table 2 (more details on the comparison can be fo”
Next-generation sequencing: from basic research to diagnostics. (2009, background): “Software for de novo assembly includes Edina ( 70 ), EULER-SR (74), SHARCGS (75), SSAKE (69), Velvet (76), and SOAPdenovo (http://soap.genomics.org.cn/).”
De novo fragment assembly with short mate-paired reads: Does the read length matter? (2009, positive): “We compared five recently published de novo short read assemblers aimed at short reads: SSAKE [29], SHARCGS [6], VCAKE [16], Edena [11], and Velvet [32].”
Assembly Algorithms for Next-Generation Sequencing Data (2010, positive): “The Edena software [47] discards duplicate reads and finds all perfect, error-free, overlaps.”
Genome assembly reborn: recent computational challenges (2009, background): “assembly graph [8, 28] —or by adding to the graph”
De novo transcriptome assembly with ABySS (2009, methodology): “…sequencing technologies are increasingly being employed for characterizing genomes (Bentley et al., 2008; Dohm et al. 2007; Farrer et al., 2009; Hernandez et al. 2008; Kozarewa et al., 2009; Ossowski et al. 2008; Salzberg et al., 2008; Warren et al., 2009) and transcriptomes (Fullwood et al.,…”
Bacillus thuringiensis Toxins: An Overview of Their Biocidal Activity (2014, positive): “Sequences can readily be assembled in contigs using a regular desktop computer [160] with de novo assembly tools bundled in bioinformatic software, such as CLC Genomics Workbench or Geneious Pro (both commercial software), or using diverse open source assemblers freely available in the BioLinux dist”
A window into third-generation sequencing. (2010, methodology): “A number of assemblers for de novo assembly have been written for SGS, including overlap graph approaches in which contigs are assembled by looking at sequence overlaps, like Edna (46), VCAKE (47) and SHARCGS (48); those based on the de Bruijn graph data structure (49), like Velvet (50), EULER-SR (5”
Assemblathon 1: a competitive assessment of de novo short read assembly methods. (2011, background): “, Hubisz et al. 2011), and Exonerate (Hernandez et al. 2008; Zerbino and Birney 2008). Given such an alignment, most simply, the proportion of a reference’s coverage can be reported (Li et al. 2010b; Zhang et al. 2011). Notably, Gnerre et al. (2011) compared novel short-read assemblies with the huma”