Supporting data and materials for the de novo assembly of Dekkera bruxellensis CBS11270 using multiple technologies.
Dataset type: Genomic, Genome-Mapping, Software
Data released on November 04, 2015
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.
Read the peer-reviewed publication(s):
Olsen, R.-A., Bunikis, I., Tiukova, I., Holmberg, K., Lötstedt, B., Pettersson, O. V., … 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). doi:10.1186/s13742-015-0094-1
Accessions (data included in GigaDB):
|Sample ID||Taxonomic ID||Common Name||Genbank Name||Scientific Name||Sample Attributes|
|CBS11270||5007||Brettanomyces bruxellensis||Dekkera bruxellensis|| Alternative names:Dekkera bruxellensis|
Reference for biomaterial:doi:10.1007/s00253-010-2...
... Alternative names:Dekkera bruxellensis
Reference for biomaterial:doi:10.1007/s00253-010-2619-y