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Data released on March 25, 2015

Supporting materials for "Bacterial and viral identification and differentiation by amplicon7 sequencing on the MinION nanopore sequencer".

Corriveau, E, J; Haas, J, L; Kadavy, D, R; Kilianski, A; Liem, A, T; Minot, S, S; Rosenzweig, C; Willis, K, L (2015): Supporting materials for "Bacterial and viral identification and differentiation by amplicon7 sequencing on the MinION nanopore sequencer". GigaScience Database. http://dx.doi.org/10.5524/100134 RIS BibTeX Text

The MinION nanopore sequencer was recently released to a community of alpha-testers for evaluation using a variety of sequencing applications. Recent reports have tested the ability of the MinION to act as a whole genome sequencer and have demonstrated that nanopore sequencing has tremendous potential utility. However, the current nanopore technology still has limitations with respect to error-rate, and this is problematic when attempting to assemble whole genomes without secondary rounds of sequencing to correct errors. In this study, we tested the ability of the MinION nanopore sequencer to accurately identify and differentiate bacterial and viral samples via directed sequencing of characteristic genes shared broadly across a target clade. Using a 6 hour sequencing run time, sufficient data were generated to identify an E. coli sample down to the species level from 16S rDNA amplicons. Three poxviruses (cowpox, vaccinia-MVA, and vaccinia-Lister) were identified and differentiated down to the strain level, despite over 98% identity between the vaccinia strains.

Contact Submitter

Related manuscripts:

doi:10.1186/s13742-015-0051-z

Additional information:

https://github.com/gigascience/paper-kilianski2015

Accessions (data included in GigaDB):

ENA: ERP009678
BioProject: PRJEB8656

Genomic

http://gigadb.org/images/data/cropped/100134_minion.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Cowpox10243  Cowpox virus
E.coli-K1283333  Escherichia coli K-12
Vaccinia-Lister10252  Vaccinia virus Lister
Vaccinia-MVA332193  Vaccinia Virus Acambis 3000 MVA
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 
OtherUNKNOWN7.43 MB2015-03-09
OtherTEXT883.7 KB2015-03-09
Amplicon sequenceFASTA11.21 MB2015-03-09
OtherFASTA1.03 MB2015-03-09
OtherUNKNOWN0.43 KB2015-03-09
OtherUNKNOWN27.66 KB2015-03-09
OtherUNKNOWN27.66 KB2015-03-09
OtherUNKNOWN41.33 MB2015-03-09
OtherUNKNOWN10.34 MB2015-03-09
ScriptUNKNOWN0.39 KB2015-03-09
Displaying 1-10 of 119 File(s).

History:

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