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Scientific article
Open access
English

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

Published inBioinformatics, vol. 30, no. 1, p. 40-49
Publication date2014
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
  • Algorithms
  • Base Sequence
  • Chromosome Mapping/methods
  • Genome
  • Genomics/methods
  • High-Throughput Nucleotide Sequencing/methods
  • Molecular Sequence Data
  • Sequence Analysis, DNA/methods
  • Software
  • Staphylococcus aureus/genetics
Citation (ISO format)
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. 40–49. doi: 10.1093/bioinformatics/btt590
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Article (Published version)
accessLevelPublic
Identifiers
ISSN of the journal1367-4803
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375downloads

Technical informations

Creation07/24/2014 11:29:00 AM
First validation07/24/2014 11:29:00 AM
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