Tim Walker explained quality control of metagenomic assemblies as part of the Nanopore Learning Metagenomics course. They spoke about the metrics to determine confidence in assembly model and the information it gives. Walker stated: “… what is truth, and what is artifact” to emphasize the use of metrics for metagenomic assembly quality control. Walker explained the concept of N50 value that represents the longest contigs which contain fifty percent of a particular genome. Completeness is the presence or absence of gene orthologs, genes in different species evolved from a common ancestor that are used as phylogenetic markers. Programs may detect orthologs of different species as potential contaminants. BUSCO and CheckM are used. CheckM can estimate rates of chimeras and contamination. Standardized metrics have been developed by the Genomic Standards Consortium (GSC) to measure and assess quality. MetaQUAST evaluates metagenomic assemblies based on alignments of the MAGs to close references. It is a metagenome-specific version of QUAST. MetaQUAST will detect likely species from your data and download references from NCBI. Genome completeness is assessed by the detection of expected orthologs using the BUSCO tool. MetaQUAST, Walker noted, can be used to compare multiple assemblies, tools, and workflows. CheckM requires the user to bin contigs before analysis. The input file is a fasta files of contigs that have been pre binned. Completeness of contigs is assessed through predicting single-copy orthologs expected for data. Bandage is used to visualize de novo assembly graphs displaying connections between contigs not seen in fasta output. It can be used to highlight specific sequences and then perform BLAST searches. Bandage can assess and compare the quality of assemblies by allowing the user to visually inspect graphs of assemblies. This video was only seven minutes long but very dense. I watched it last night and again tonight, learning more about how BUSCO and MetaQUAST work.
