The next lesson in the Nanopore Learning Metagenomics course that I watched tonight was “Introduction to metagenomic assembly.” Tim Walker from the Technical Services Group at ONT introduced metagenomic assembly as reconstruction of reads into corresponding genomes. Metagenomic assembly is a computational process, said Walker, and the contigs may resemble the genomes or plasmids. Metagenome Assembled Genomes known as MAGs offer unbiased detection, more accurate taxonomic resolution, metagenomic function profiling, and antibiotic resistance profiles. Metagenomic assembly is similar to assembly of single genomes and also challenges. Some challenges of metagenomic assembly are: coverage variability, intergenome complexity and shared features, greater computational requirements… Long reads can help assemble complete genomes from metagenomic samples. The assembly of complete MAGs can offer more accurate downstream analyses. One example Walker showed was the use of long-read metagenome assembly to assemble complete bacterial genomes. Some of the approaches are the reference sequence in which reads are compared to the reference. The more suitable approach is the de novo approach to assemble bacterial genomes. MetaFlye is one assembler discussed that has an option for metagenomes. In a second video, Walker introduced quality control of assembled genomes from microbial communities. I had to watch this one again tonight to learn more about metagenome assembly. CheckM assesses completeness of the genomes similar organisms. Walked noted that it can can be used to assess a MAG and could be used with Bandage, to learn about the assembly process.
