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

Dataset type: Genomic, Software, Genome-Mapping
Data released on November 04, 2015

Olsen R; Bunikis I; Tiukova I; Holmberg K; Lotstedt B; Pettersson OV; Passoth V; Kaller M; Vezzi F (2015): Supporting data and materials for the de novo assembly of Dekkera bruxellensis CBS11270 using multiple technologies. GigaScience Database. http://dx.doi.org/10.5524/100179

DOI10.5524/100179

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.

Additional details

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

Additional information:

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

Accessions (data generated as part of this study):

ENA: ERP012947





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
CBS112705007Brettanomyces bruxellensis Dekkera bruxellensis Alternative names:Dekkera bruxellensis
Isolate:CBS11270
Reference for biomaterial:doi:10.1007/s00253-010-2...
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Displaying 1-1 of 1 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Sequence assemblyFASTA4.96 MB2015-11-02
Sequence assemblyFASTA3.85 MB2015-11-02
Sequence assemblyFASTA3.95 MB2015-11-02
Sequence assemblyFASTA3.85 MB2015-11-02
Sequence assemblyFASTA4.21 MB2015-11-02
MetadataXML142.02 KB2015-11-02
TextTAR55.87 KB2015-11-02
Sequence assemblyFASTA3.69 MB2015-11-02
MetadataXML120.54 KB2015-11-02
Sequence assemblyFASTA3.01 MB2015-11-02
Displaying 1-10 of 16 File(s).
Date Action
November 4, 2015 Dataset publish
November 27, 2015 Manuscript Link added : 10.1186/s13742-015-0094-1