Paired-end read length lower bounds for genome re-sequencing

Rayan Chikhi 1 Dominique Lavenier 1
1 SYMBIOSE - Biological systems and models, bioinformatics and sequences
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, Inria Rennes – Bretagne Atlantique
Abstract : Next-generation sequencing technology is enabling massive production of high-quality paired-end reads. Many platforms (Illumina Genome Analyzer, Applied Biosystems SOLID, Helicos HeliScope) are currently able to produce "ultra-short" paired reads of lengths starting at 25 nt. An analysis by Whiteford et al. [1] on sequencing using unpaired reads shows that ultra-short reads theoretically allow whole genome re-sequencing and de novo assembly of only small eukaryotic genomes. By conducting an analysis extending Whiteford et al. results, we investigate to what extent genome re-sequencing is feasible with ultra-short paired reads. We obtain theoretical read length lower bounds for re-sequencing that are also applicable to paired-end de novo assembly.
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Rayan Chikhi, Dominique Lavenier. Paired-end read length lower bounds for genome re-sequencing. BMC Bioinformatics, BioMed Central, 2009, ⟨10.1186/1471-2105-10-S13-O2⟩. ⟨inria-00426856⟩

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