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Data released on June 16, 2017

Supporting data for "Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION portable nanopore sequencer"

Benitez-Paez, A; Sanz, Y (2017): Supporting data for "Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION portable nanopore sequencer" GigaScience Database. http://dx.doi.org/10.5524/100312 RIS BibTeX Text

The miniaturised and portable DNA sequencer MinIONTM has demonstrated great potential in different analyses such as genome-wide sequencing, pathogen outbreak detection and surveillance, human genome variability, and microbial diversity. In this study, we tested the ability of the MinIONTM platform to perform long amplicon sequencing in order to design new approaches to study microbial diversity using a multi-locus approach.
After compiling a robust database by parsing and extracting the rrn bacterial region from more than 67,000 complete or draft bacterial genomes, we demonstrated that the data obtained during sequencing of the long amplicon in the MinIONTM device using R9 and R9.4 chemistries was sufficient to study two mock microbial communities in a multiplex manner and to almost completely reconstruct the microbial diversity contained in the HM782D and D6305 mock communities.
Although nanopore-based sequencing produces reads with lower per-base accuracy compared with other platforms, we presented a novel approach consisting of multi-locus and long amplicon sequencing using the MinION MkIb DNA sequencer and R9 and R9.4 chemistries that help to overcome the main disadvantage of this portable sequencing platform. Furthermore, the nanopore sequencing library constructed with the last releases of pore chemistry (R9.4) and sequencing kit (SQK-LSK108) permitted to retrieve the higher level of 1D read accuracy sufficient to characterize the microbial species present in each mock community analysed. Improvements in nanopore chemistry, such as minimising base-calling errors and new library protocols able to produce rapid 1D libraries, will provide more reliable information in near future. Such data will be useful for more comprehensive and faster specific detection of microbial species and strains in complex ecosystems.

Contact Submitter

Accessions (data included in GigaDB):

BioProject: PRJEB15264

Genomic

http://gigadb.org/images/data/cropped/100312.jpg

Funding:

  • Funding body - European Union Seventh Framework Programme
  • Award ID - 613979
  • Awardee - Y Sanz

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
D6305-rrn1303873  bacterial mixed DNA library Description:PCR of the 16S-ITS-23S bacterial regio...
Alternative accession-BioSample:SAMEA4413455
Reference for biomaterial:ZymoBIOMICS (www.zymores...
...
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D6305-v4v51303873  bacterial mixed DNA library Description:PCR of the V4-V5 bacterial 16S rRNA ge...
Alternative accession-BioSample:SAMEA4413455
Reference for biomaterial:ZymoBIOMICS (www.zymores...
...
+
HM782D-rrn1303873  bacterial mixed DNA library Description:PCR of the 16S-ITS-23S bacterial regio...
Alternative accession-BioSample:SAMEA4413456
Reference for biomaterial:BEI Resources (www.beire...
...
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HM782D-v4v51303873  bacterial mixed DNA library Description:PCR of the V4-V5 bacterial 16S rRNA ge...
Alternative accession-BioSample:SAMEA4413456
Reference for biomaterial:BEI Resources (www.beire...
...
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Displaying 1-4 of 4 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 
fastaFASTA3.74 MB2017-06-09
fastaFASTA3.25 MB2017-06-09
fastaFASTA2.92 MB2017-06-09
fastaFASTA2.48 MB2017-06-09
unknownUNKNOWN0.1 KB2017-06-09
fastaFASTA3.24 MB2017-06-09
unknownFASTA3.23 MB2017-06-09
unknownTAR24.02 MB2017-06-09
ReadmeTEXT3.56 KB2017-06-09
Mixed archivearchive28.33 MB2017-06-09
Displaying 1-10 of 11 File(s).

History:

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