Benchmarking bioinformatic tools for amplicon-based sequencing of norovirus
Creators
- 1. Teagasc Food Research Centre
- 2. Marine Institute
- 3. 0000-0002-8726-0328
- 4. 0000-0002-5465-9068
Description
This repository contains associated datasets and accession numbers for a study entitled 'Benchmarking bioinformatic tools for amplicon-based sequencing of norovirus'. The scripts for this project can be found on the GitHub project page.
Expected composition tsv files are the OTU tables for each simulation performed (001-010). OTU IDs in this case are the expected taxonomy with the associated accession numbers. Samples are numbered 1-40, including the simulation number. Expected sequences fasta files contain the sequences used as input for each simulation, without primers or Illumina adapter sequences.
Amplicons were generated using the following primers:
GI Primers
GISKF: CTG CCC GAA TTY GTA AAT GA 4
GISKR: CCA ACC CAR CCA TTR TAC A 5
GII Primers
G2SKF: CNT GGG AGG GCG ATC GCAA 8
G2SKR: CCR CCN GCA TRH CCR TTR TAC AT
In this study, three databases and multiple classifiers were compared. Here we include the taxonomy and fasta files for each database; noronet =NoroNet RIVM, calicinet= HuCat CDC and custom, randomly generated database. Fasta files for the classifiers include the GI/GII primers listed above in a 5-3 orientation.
The tags.txt file contains the Illumina adapters used for the simulation component of the study.
Files
tags.txt
Files
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Additional details
References
- lant in Tokyo, Japan. Water Sci Technol. 2006;54(11–12):301–8. 37. Kitajima M, Haramoto E, Phanuwan C, Katayama H, Ohgaki S. Detection of genogroup IV norovirus in wastewater and river water in Japan. Lett Appl Microbiol. 2009;49(5):655–8.
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- Tatusov RL, Chhabra P, Diez-Valcarce M, Barclay L, Cannon JL, Vinjé J. Human Calicivirus Typing tool: A web-based tool for genotyping human norovirus and sapovirus sequences. J Clin Virol. 2020 Dec 13;104718.