Tim Walker from the Technical Services Team with Oxford Nanopore Technologies presented the Nanopore Learning Course – Metagenomics lesson I watched tonight. They spoke about metagenomic classification techniques to identify organisms from sequence data and annotate genes. For targeted metagenomics, ITS, 16S, or antibiotic resistance genes can be amplified and sequenced. Whole genome sequencing can also be used to study metagenomes. With long-read ONT reads, direct read mapping to a database can be performed. Alternatively, reads can be assembled into MAGs and mapped to a database. While this process is more computationally intensive, it can provide additional information. The databases used are critical, Walker emphasized. They suggested using curated databases and noting that databases are finite. Walker noted that read-based taxonomic binning using databases should consider the possibility of false positives and false negatives. Sensitivity and precision in classification is influenced by choice of algorithm, database size, and computational capacity, explained Walker. The next session was an introduction to EPI2ME WIMP workflows for metagenomic analyses and antimicrobial resistance gene identification. I continue learning from the ONT Learning Courses though some of the EPI2ME content is outdated.
