Benchmarking bioinformatic tools for amplicon-based sequencing of norovirus

<p>This repository contains associated datasets and accession numbers for a study entitled &#39;<strong>Benchmarking bioinformatic tools for amplicon-based sequencing of norovirus&#39;</strong>. The scripts for this project can be found on the GitHub project<a href="https://github.com/ahfitzpa/Benchmarking-bioinformatics-norovirus-amplicons">&nbsp;page</a>.&nbsp;</p> <p>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&nbsp;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.</p> <p>Amplicons were generated using the following primers:</p> <p><strong>GI Primers&nbsp;</strong><br> GISKF: CTG CCC GAA TTY GTA AAT GA 4<br> GISKR: CCA ACC CAR CCA TTR TAC A 5<br> <br> <strong>GII Primers&nbsp;</strong><br> G2SKF: CNT GGG AGG GCG ATC GCAA 8<br> G2SKR: CCR CCN GCA TRH CCR TTR TAC AT</p> <p>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.&nbsp;</p> <p>The tags.txt file&nbsp;contains the Illumina adapters used for the simulation component of the study.</p>