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RESEARCH ARTICLE Open Access Sequencing of BAC pools by different next generation sequencing platforms and strategies
BibTeX
@MISC{Taudien_researcharticle,
author = {Stefan Taudien and Burkhard Steuernagel and Ruvini Ariyadasa and Daniela Schulte and Thomas Schmutzer and Marco Groth and Marius Felder and Andreas Petzold and Uwe Scholz and Klaus Fx Mayer and Nils Stein and Matthias Platzer},
title = {RESEARCH ARTICLE Open Access Sequencing of BAC pools by different next generation sequencing platforms and strategies},
year = {}
}
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Abstract
Background: Next generation sequencing of BACs is a viable option for deciphering the sequence of even large and highly repetitive genomes. In order to optimize this strategy, we examined the influence of read length on the quality of Roche/454 sequence assemblies, to what extent Illumina/Solexa mate pairs (MPs) improve the assemblies by scaffolding and whether barcoding of BACs is dispensable. Results: Sequencing four BACs with both FLX and Titanium technologies revealed similar sequencing accuracy, but showed that the longer Titanium reads produce considerably less misassemblies and gaps. The 454 assemblies of 96 barcoded BACs were improved by scaffolding 79 % of the total contig length with MPs from a non-barcoded library. Assembly of the unmasked 454 sequences without separation by barcodes revealed chimeric contig formation to be a major problem, encompassing 47 % of the total contig length. Masking the sequences reduced this fraction to 24%. Conclusion: Optimal BAC pool sequencing should be based on the longest available reads, with barcoding essential for a comprehensive assessment of both repetitive and non-repetitive sequence information. When interest is restricted to non-repetitive regions and repeats are masked prior to assembly, barcoding is non-essential. In any case, the assemblies can be improved considerably by scaffolding with non-barcoded BAC pool MPs.
Keyphrases
different next generation bac pool research article open access sequencing total contig length titanium technology available read non-repetitive sequence information non-barcoded bac pool mp non-barcoded library similar sequencing accuracy major problem extent illumina solexa mate pair repetitive genome optimal bac pool sequencing chimeric contig formation viable option read length non-repetitive region comprehensive assessment sequence assembly next generation sequencing barcoded bacs
