title: De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping.
abstract: BACKGROUND
  It remains a challenge to perform de novo assembly using next-generation sequencing (NGS). Despite the availability of multiple sequencing technologies and tools (e.g., assemblers) it is still difficult to assemble new genomes at chromosome resolution (i.e., one sequence per chromosome). Obtaining high quality draft assemblies is extremely important in the case of yeast genomes to better characterise major events in their evolutionary history. The aim of this work is two-fold: on the one hand we want to show how combining different and somewhat complementary technologies is key to improving assembly quality and correctness, and on the other hand we present a de novo assembly pipeline we believe to be beneficial to core facility bioinformaticians. To demonstrate both the effectiveness of combining technologies and the simplicity of the pipeline, here we present the results obtained using the Dekkera bruxellensis genome.
  
  
  METHODS
  In this work we used short-read Illumina data and long-read PacBio data combined with the extreme long-range information from OpGen optical maps in the task of de novo genome assembly and finishing. Moreover, we developed NouGAT, a semi-automated pipeline for read-preprocessing, de novo assembly and assembly evaluation, which was instrumental for this work.
  
  
  RESULTS
  We obtained a high quality draft assembly of a yeast genome, resolved on a chromosomal level. Furthermore, this assembly was corrected for mis-assembly errors as demonstrated by resolving a large collapsed repeat and by receiving higher scores by assembly evaluation tools. With the inclusion of PacBio data we were able to fill about 5 % of the optical mapped genome not covered by the Illumina data.
authors.affiliation: Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden.
authors.forename: Remi-Andre
authors.initials: RA
authors.lastname: Olsen
authors.affiliation: Uppsala Genome Center, NGI/SciLifeLab, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, SE-752 37 Uppsala, Sweden.
authors.forename: Ignas
authors.initials: I
authors.lastname: Bunikis
authors.affiliation: Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, SE-75007 Uppsala, Sweden.
authors.forename: Ievgeniia
authors.initials: I
authors.lastname: Tiukova
authors.affiliation: Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden.
authors.forename: Kicki
authors.initials: K
authors.lastname: Holmberg
authors.affiliation: Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden.
authors.forename: Britta
authors.initials: B
authors.lastname: Lötstedt
authors.affiliation: Uppsala Genome Center, NGI/SciLifeLab, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, SE-752 37 Uppsala, Sweden.
authors.forename: Olga Vinnere
authors.initials: OV
authors.lastname: Pettersson
authors.affiliation: Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, SE-75007 Uppsala, Sweden.
authors.forename: Volkmar
authors.initials: V
authors.lastname: Passoth
authors.affiliation: Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden.
authors.forename: Max
authors.initials: M
authors.lastname: Käller
authors.affiliation: Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden.
authors.forename: Francesco
authors.initials: F
authors.lastname: Vezzi
mesh_terms: D002874:Chromosome Mapping / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D055167:Dekkera / Q000235:genetics*; D016681:Genome, Fungal; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software