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Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
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2014 (English)In: BMC Genomics, ISSN 1471-2164, Vol. 15, no 1, 439- p.Article in journal (Refereed) Published
Abstract [en]

Background: Sampling genomes with Fosmid vectors and sequencing of pooled Fosmid libraries on the Illumina platform for massive parallel sequencing is a novel and promising approach to optimizing the trade-off between sequencing costs and assembly quality. Results: In order to sequence the genome of Norway spruce, which is of great size and complexity, we developed and applied a new technology based on the massive production, sequencing, and assembly of Fosmid pools (FP). The spruce chromosomes were sampled with similar to 40,000 bp Fosmid inserts to obtain around two-fold genome coverage, in parallel with traditional whole genome shotgun sequencing (WGS) of haploid and diploid genomes. Compared to the WGS results, the contiguity and quality of the FP assemblies were high, and they allowed us to fill WGS gaps resulting from repeats, low coverage, and allelic differences. The FP contig sets were further merged with WGS data using a novel software package GAM-NGS. Conclusions: By exploiting FP technology, the first published assembly of a conifer genome was sequenced entirely with massively parallel sequencing. Here we provide a comprehensive report on the different features of the approach and the optimization of the process. We have made public the input data (FASTQ format) for the set of pools used in this study: accessible via software used for running the assembly process is available at

Place, publisher, year, edition, pages
2014. Vol. 15, no 1, 439- p.
National Category
Biological Sciences
URN: urn:nbn:se:kth:diva-148298DOI: 10.1186/1471-2164-15-439ISI: 000338258700001ScopusID: 2-s2.0-84902553599OAI: diva2:736538
Knut and Alice Wallenberg FoundationScience for Life Laboratory - a national resource center for high-throughput molecular bioscience

QC 20140807

Available from: 2014-08-07 Created: 2014-08-05 Last updated: 2014-08-07Bibliographically approved

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Alexeyenko, AndreyLundeberg, Joakim
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Gene TechnologyScience for Life Laboratory, SciLifeLab
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