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Title

De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads

Authors
Tewhey, Ryan
Veyrieras, Jean-Baptiste
Østerås, Magne
Published in Bioinformatics. 2014, vol. 30, no. 1, p. 40-9
Abstract Paired-end sequencing allows circumventing the shortness of the reads produced by second generation sequencers and is essential for de novo assembly of genomes. However, obtaining a finished genome from short reads is still an open challenge. We present an algorithm that exploits the pairing information issued from inserts of potentially any length. The method determines paths through an overlaps graph by using a constrained search tree. We also present a method that automatically determines suited overlaps cutoffs according to the contextual coverage, reducing thus the need for manual parameterization. Finally, we introduce an interactive mode that allows querying an assembly at targeted regions.
Keywords AlgorithmsBase SequenceChromosome Mapping/methodsGenomeGenomics/methodsHigh-Throughput Nucleotide Sequencing/methodsMolecular Sequence DataSequence Analysis, DNA/methodsSoftwareStaphylococcus aureus/genetics
Identifiers
PMID: 24130309
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Article (Published version) (506 Kb) - public document Free access
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Research group Analyse génomique et fonctionnelle du staphylocoque doré (604)
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HERNANDEZ, David et al. De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads. In: Bioinformatics, 2014, vol. 30, n° 1, p. 40-9. https://archive-ouverte.unige.ch/unige:40259

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Deposited on : 2014-09-18

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