Supporting data for "A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data."

Dataset type: Genomic
Data released on November 30, 2015

Risse J; Thomson M; Patrick S; Blakely G; Koutsovoulos G; Blaxter M; Watson M (2015): Supporting data for "A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data." GigaScience Database. http://dx.doi.org/10.5524/100177

DOI10.5524/100177

Second and third generation sequencing technologies have revolutionised bacterial genomics. Short-read Illumina reads result in cheap but fragmented assemblies, whereas longer reads are more expensive but result in more complete genomes. The Oxford Nanopore MinION device is a revolutionary mobile sequencer that can produce thousands of long, single molecule reads.
We sequenced Bacteroides fragilis strain BE1 using both the Illumina MiSeq and Oxford Nanopore MinION platforms. We were able to assemble a single chromosome of 5.18 Mb, with no gaps, using publicly available software and commodity computing hardware. We identified gene rearrangements and the state of invertible promoters in the strain.
The final assembly and annotations are available from the public archives (EBI/NCBI/DDBJ) and additionally here we provide the assemblies done for comparison from each of the individual technologies and the alignments of the original raw reads to the final assembly.

Additional details

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Accessions (data generated as part of this study):

BioProject: PRJEB10044





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMEA3494626817  Bacteroides fragilis Description:Bacteroides fragilis; B. fragilis stra...
Isolate:BE1
Sequencing method:Illumina MiSeq
...
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SAMEA3498576817  Bacteroides fragilis Description:Bacteroides fragilis; B.fragilis GB297...
Isolate:BE1
Sequencing method:MinION
...
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Displaying 1-2 of 2 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
SAMEA3498576AlignmentsBAM54.95 MB2015-11-23
SAMEA3498576OtherBAI23.22 KB2015-11-23
SAMEA3494626Sequence assemblyFASTA5 MB2015-11-23
SAMEA3494626AlignmentsBAM290.88 MB2015-11-23
SAMEA3494626OtherBAI16.77 KB2015-11-23
ReadmeTEXT1.58 KB2015-11-23
ImagePNG145.11 KB2015-11-23
ImagePNG126.61 KB2015-11-23
ImagePNG128.91 KB2015-11-23
Displaying 1-9 of 9 File(s).
Funding body Awardee Award ID Comments
Biotechnology and Biological Sciences Research Council BS/E/D/20310000
Biotechnology and Biological Sciences Research Council BB/J004243/1
Biotechnology and Biological Sciences Research Council BB/M020037/1
Natural Environment Research Council R8/H10/56
Medical Research Council MR/K001744/1
Date Action
November 27, 2015 Dataset publish
December 29, 2015 Manuscript Link added : 10.1186/s13742-015-0101-6