title: Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools.
abstract: 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 ~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:ftp://congenie.org/congenie/Nystedt_2013/Assembly/ProcessedData/FosmidPools/.(alternatively accessible via http://congenie.org/downloads).The software used for running the assembly process is available at http://research.scilifelab.se/andrej_alexeyenko/downloads/fpools/.
authors.forename: Andrey
authors.initials: A
authors.lastname: Alexeyenko
authors.forename: Björn
authors.initials: B
authors.lastname: Nystedt
authors.forename: Francesco
authors.initials: F
authors.lastname: Vezzi
authors.forename: Ellen
authors.initials: E
authors.lastname: Sherwood
authors.forename: Rosa
authors.initials: R
authors.lastname: Ye
authors.forename: Bjarne
authors.initials: B
authors.lastname: Knudsen
authors.forename: Martin
authors.initials: M
authors.lastname: Simonsen
authors.forename: Benjamin
authors.initials: B
authors.lastname: Turner
authors.forename: Pieter
authors.initials: P
authors.lastname: de Jong
authors.forename: Cheng-Cang
authors.initials: CC
authors.lastname: Wu
authors.affiliation: School of Biotechnology, Science for Life Laboratory, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden. joakim.lundeberg@scilifelab.se.
authors.forename: Joakim
authors.initials: J
authors.lastname: Lundeberg
mesh_terms: D003001:Cloning, Molecular; D005822:Genetic Vectors; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics / Q000379:methods*; D028222:Picea / Q000235:genetics*; D012984:Software