Supporting data for "de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer"

Dataset type: Genomic
Data released on December 23, 2016

Istace B; Friedrich A; d’Agata L; Faye S; Payen E; Beluche O; Caradec C; Davidas S; Cruaud C; Liti G; Lemainque A; Engelen S; Wincker P; Schacherer J; Aury JM (2016): Supporting data for "de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer" GigaScience Database. http://dx.doi.org/10.5524/100263

DOI10.5524/100263

Oxford Nanopore Technologies Ltd (Oxford, UK) have recently commercialized MinION, a small single-molecule nanopore sequencer, that offers the possibility of sequencing long DNA fragments from small genomes in a matter of seconds. The Oxford Nanopore technology is truly disruptive, it has the potential to revolutionize genomic applications due to its portability, low-cost, and ease of use compared with existing long reads sequencing technologies. The MinION sequencer enables the rapid sequencing of small eukaryotic genomes, such as the yeast genome. Combined with existing assembler algorithms, near complete genome assemblies can be generated and comprehensive population genomic analyses can be performed.
Here, we resequenced the genome of the Saccharomyces cerevisiae S288C strain to evaluate the performance of nanopore-only assemblers. Then we de novo sequenced and assembled the genomes of 21 isolates representative of the S. cerevisiae genetic diversity using the MinION platform. The contiguity of our assemblies was 14 times higher than the Illumina-only assemblies and we obtained one or two long contigs for 65% of the chromosomes. This high contiguity allowed us to accurately detect large structural variations across the 21 studied genomes.
Because of the high completeness of the nanopore assemblies, we were able to produce a complete cartography of transposable elements insertions and inspect structural variants that are generally missed using a short-read sequencing strategy.

Additional details

Read the peer-reviewed publication(s):

Istace, B., Friedrich, A., d’ Agata, L., Faye, S., Payen, E., Beluche, O., … Aury, J.-M. (2017). de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer. GigaScience, 6(2). doi:10.1093/gigascience/giw018

Accessions (data generated as part of this study):

BioProject: PRJEB14774





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
ABH1337530  Saccharomyces cerevisiae Description:YJM454_1b, Saccharomyces cerevisiae, i...
Alternative accession-BioSample:SAMEA3894921
Source material identifiers:Not Applicable
...
+
ADM929629Saccharomyces cerevisiae CLIB324Saccharomyces cerevisiae CLIB324 Description:CLIB324_2, Saccharomyces cerevisiae, i...
Alternative accession-BioSample:SAMEA3894961
Source material identifiers:Not Applicable
...
+
ADQ4932brewer's yeastbaker's yeastSaccharomyces cerevisiae Description:K12_2, Saccharomyces cerevisiae, isola...
Alternative accession-BioSample:SAMEA3894964
Source material identifiers:Not Applicable
...
+
ADS471859  Saccharomyces cerevisiae Description:T73_1b, Saccharomyces cerevisiae, isol...
Alternative accession-BioSample:SAMEA3894966
Source material identifiers:Not Applicable
...
+
AEG4932brewer's yeastbaker's yeastSaccharomyces cerevisiae Description:CBS7962, Saccharomyces cerevisiae, iso...
Alternative accession-BioSample:SAMEA3894974
Source material identifiers:Not Applicable
...
+
AKR4932brewer's yeastbaker's yeastSaccharomyces cerevisiae Description:CLQCA_05-006, Saccharomyces cerevisiae...
Alternative accession-BioSample:SAMEA3895070
Source material identifiers:Not Applicable
...
+
ANE4932brewer's yeastbaker's yeastSaccharomyces cerevisiae Description:YPS134, Saccharomyces cerevisiae, isol...
Alternative accession-BioSample:SAMEA3895112
Source material identifiers:Not Applicable
...
+
ASN4932brewer's yeastbaker's yeastSaccharomyces cerevisiae Description:CLIB630, Saccharomyces cerevisiae, iso...
Alternative accession-BioSample:SAMEA3895186
Source material identifiers:Not Applicable
...
+
AVB4932brewer's yeastbaker's yeastSaccharomyces cerevisiae Description:CECT10266, Saccharomyces cerevisiae, i...
Alternative accession-BioSample:SAMEA3895205
Source material identifiers:Not Applicable
...
+
BAH4932brewer's yeastbaker's yeastSaccharomyces cerevisiae Description:SX3, Saccharomyces cerevisiae, isolate...
Alternative accession-BioSample:SAMEA3895227
Source material identifiers:Not Applicable
...
+
Displaying 1-10 of 22 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
annotationGFF37.38 KB2016-12-20
DirectoryUNKNOWN256.38 MB2016-12-20
tabular dataTEXT421.45 KB2016-12-20
ReadmeTEXT1.76 KB2016-12-20
tabular dataTSV2.29 KB2016-12-20
DirectoryUNKNOWN16.46 KB2016-12-20
DirectoryUNKNOWN15.73 KB2016-12-20
DirectoryUNKNOWN7.8 KB2016-12-20
DirectoryUNKNOWN6.15 KB2016-12-20
DirectoryUNKNOWN5.09 KB2016-12-20
Displaying 1-10 of 10 File(s).

Protocols.io:

Date Action
December 23, 2016 Dataset publish
January 6, 2017 External Link added : 0.17504/protocols.io.gvxbw7n
January 6, 2017 External Link updated : http://doi.org/0.17504/protocols.io.gvxbw7n
January 9, 2017 Manuscript Link added : 10.1093/gigascience/giw018
January 17, 2017 External Link updated : http://doi.org/10.17504/protocols.io.gvxbw7n