Benchmarking bioinformatic tools for amplicon-based sequencing of norovirus

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.