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Data released on November 30, 2015

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

Blakely, G; Blaxter, M; Koutsovoulos, G; Patrick, S; Risse, J; Thomson, 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 RIS BibTeX Text

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.

Contact Submitter

Related manuscripts:

doi:10.1186/s13742-015-0101-6

Accessions (data included in GigaDB):

BioProject: PRJEB10044

Keywords:

MinION, Illumina, NGS, assembly, 

Genomic

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Funding:

  • Funding body - Biotechnology and Biological Sciences Research Council
  • Award ID - BS/E/D/20310000
  • Funding body - Biotechnology and Biological Sciences Research Council
  • Award ID - BB/J004243/1
  • Funding body - Biotechnology and Biological Sciences Research Council
  • Award ID - BB/M020037/1
  • Funding body - Natural Environment Research Council
  • Award ID - R8/H10/56
  • Funding body - Medical Research Council
  • Award ID - MR/K001744/1

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

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).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile 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).

History:

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