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Data released on January 14, 2016

Supporting data for "Species level resolution of 16S rRNA gene amplicons sequenced through MinION portable nanopore sequencer".

Benitez-Paez, A; Portune, K, J; Sanz, Y (2016): Supporting data for "Species level resolution of 16S rRNA gene amplicons sequenced through MinION portable nanopore sequencer". GigaScience Database. http://dx.doi.org/10.5524/100185 RIS BibTeX Text

The miniaturized and portable DNA sequencer MinION has been released to the scientific community in the framework of an early access programme to evaluate its application for a wide variety of genetic approaches. This technology has demonstrated a great potential, especially in genome-wide analyses. In this study, we tested the ability of the MinION system to perform amplicon sequencing in order to design new approaches to study microbial diversity using nearly full-length 16S rDNA sequences.
Using the R7.3 chemistry, we generated more than 3.8 million events (nt) during a single sequencing run. This data was sufficient for reconstruction of more than 90% of the 16S rRNA gene sequences for 20 different species present in a mock community used as a reference. After read mapping and 16S rRNA gene assembly, consensus sequences and 2d reads were recovered to make taxonomy assignments down to the species level. Additionally, we were able to measure the relative abundance of all the species present in a mock community and detected a biased species distribution originating from the PCR reaction using "universal" primers.
Although nanopore-based sequencing produces reads with lower per-base accuracy in comparison with other platforms, the MinION DNA sequencer is valuable for both high taxonomic resolution and microbial diversity analysis. Improvements of the nanopore chemistry will further deliver more reliable information useful for the specific detection of microbial species and strains in complex ecosystems as a consequence of minimizing the basecalling errors and nucleotide bias as that reported here for 16S rRNA amplicon sequencing.

Contact Submitter

Related manuscripts:

doi:10.1186/s13742-016-0111-z

Additional information:

https://github.com/alfbenpa/16S_MinION

Accessions (data included in GigaDB):

BioProject: PRJEB8730

Keywords:

MinION nanopore sequencer 16S rDNA amplicon microbial diversity long-read sequencing 

Metagenomic

http://gigadb.org/images/data/cropped/100185.jpg

Funding:

  • Funding body - European Commission
  • Award ID - Contract 613979
  • Comment - MyNewGut Project

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
HM-782D1235509synthetic metagenome Source material identifiers:HM-782D
Sample source:BEI Resources (http://www.beiresourc...
Alternative accession-SRA_sample:ERS760633
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Displaying 1-1 of 1 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 
HM-782D16S rRNAFASTA1.65 KB2015-12-18
HM-782DAlignmentsSAM158.36 KB2015-12-18
HM-782D16S rRNAFASTA1.64 KB2015-12-18
HM-782DAlignmentsSAM117.46 KB2015-12-18
HM-782DOtherEXCEL199 KB2015-12-18
HM-782DOtherEXCEL199.5 KB2015-12-18
HM-782DOtherEXCEL200.5 KB2015-12-18
HM-782D16S rRNAFASTA1.6 KB2015-12-18
HM-782DAlignmentsSAM240.29 KB2015-12-18
HM-782D16S rRNAFASTA1.62 KB2015-12-18
Displaying 1-10 of 44 File(s).

History:

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