Tim Walker from the Technical Services Group conducted a demonstration of EPI2ME as part of the Nanopore Learning course. Walker noted that EPI2ME currently hosts free metagenomic classification pipelines including WIMP, the antimicrobial resistance workflow, and the Fastq 16S workflow. The 16S workflow works with the 16S barcoding kit. This is the kit and workflow we will use in the metagenomics course. Walker demonstrated how you can start a new analysis and let EPI2ME search for files in a folder that the user selects. The WIMP workflow has several parameters that can be edited. These include minimum qscore and barcoding. After submitting a job, a unique analysis ID is shared. After enough data passes the workflow, an interactive report is generated with the total number of reads and aa summary of taxonomic counts. The QC panel summarizes the metadata, output, and how many reads pass the QC threshold. Count tables can be filtered, and the taxonomy tree is generated in real-time. Static graphs and spreadsheets can be produced and downloaded.
Walker continued explaining metagenomic assembly, “the computational process of reconstructing microbial genomes within a sample.” These MAG or metagenome assembled genomes ca offer potential downstream options for analysis such as functional analysis, taxonomic identification, antimicrobial resistance gene identification, and plasmid analysis. There are challenges resolving areas of similarity and the use of computational resources. Walker emphasized that assembly tools should be used that are designed for metagenome analysis. Assembly with long-reads facilitates more complete MAGs. However, there are considerations and limitations to binning samples. Walked explained how de novo assembly is well suited for long-read sequence data and metagenomic samples. MetaFlye is based on Flye and is often used for assembly of bacterial genomes for example. MetaFlye is designed for metagenomic datasets and has several features to improve long reads. Just today I was learning about a study addressing the reliability of MAGs that I want to bring up in class.
