Supporting data and materials for the De novo assembly of Dekkera bruxellensis combining multiple-technologies using NouGAT.
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Remi-Andre Olsen; Ignas Bunikis; Ievgeniia Tiukova; Kicki Holmberg; Britta Lotstedt; Olga V Pettersson; Volkmar Passoth; Max Kaller; Francesco Vezzi
GigaScience Database. http://dx.doi.org/10.5524/100179

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 finally assembly evaluation. 
It  can be found at the following address: 
https://github.com/SciLifeLab/NouGAT/

Further details of the methods are discussed in the GigaScience article by the same authors entitled "De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping".

Files
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NouGAT-master.zip - The downloaded GitHub master file, taken as archival copy of pipeline as published, 02-Nov-2015, please visit github repository for most recent up to date version (https://github.com/SciLifeLab/NouGAT/)
abyss_asm.fa.gz - ABySS assembly
AHA_asm.fa.gz - AHA assembly
allpaths_asm.fa.gz - ALLPATHS-LG assembly
chr1-5_asm.fa.gz - Optical map guided assembly version chr1-5
chr1-7_asm.fa.gz - Optical map guided assembly version chr1-7
falcon_asm.fa.gz - FALCON assembly
hgap_asm.fa.gz - HGAP assembly
pacbiotoca_asm.fa.gz - PacBioToCA assembly
soapdenovo_asm.fa.gz - SOAPdenovo assembly
commands_logs.tar.gz - Commandline parameters, configuration files and log files
dekkera_bruxellensis_asm.fa.gz - Optical map guided assembly version 1
chr1-7_opmap.xml - Optical maps in Mapsolver XML format - chr1-7
dekkera_bruxellensis_opmap.xml - Optical maps in Mapsolver XML format - final version
filtered_subreads.fastq.gz - PacBio filtered subreads