Supporting data and materials for the de novo assembly of Dekkera bruxellensis CBS11270 using multiple technologies.

We present a genomic dataset sampled from the yeast Dekkera bruxellensis using three different technologies: Illumina short-read sequencing, PacBio long-read sequencing and optical mapping. The Illumina data consists of four different libraries of differing insert sizes (ie. paired-end fragments and mate-pair libraries), following the ALLPATHS recipe.
The purpose was to generate a draft genome assembly of high quality by combining these three different and somewhat complementary technologies. As a by-product of our work we present a pipeline for de novo assembly, NouGAT. It is a semi-automated pipeline for read pre-processing, de novo assembly with support of a wide range of assemblers and final assembly evaluation.
The version of the pipeline hosted here in GigaDB is the version as published (02-Nov-2015), for the most upto date version users are directed to the GitHub repository.

Keywords:

• genome-assembly
• assembly-evaluation
• assembly-reconciliation
• optical-maps

Read the peer-reviewed publication(s):

• Olsen, R.-A., Bunikis, I., Tiukova, I., Holmberg, K., Lötstedt, B., Pettersson, O. V., Passoth, V., Käller, M., & Vezzi, F. (2015). De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping. GigaScience, 4(1). https://doi.org/10.1186/s13742-015-0094-1

Additional information:

https://github.com/SciLifeLab/NouGAT/

Accessions (data included in GigaDB):

ENA: ERP012947