Using De Novo Metagenome Assembly for Improved Metagenomic Classification

Metagenomics is a rapidly growing field that allows for studying complex microbial communities. One of the first steps in the metagenomic analysis is the classification of the organisms present in a sample. This is usually done by comparing sequencing reads to a database of known organisms. With the recent development of long-read sequencing technologies, such as PacBio and Oxford Nanopore Technologies (ONT), it is now possible to generate highly accurate assemblies of genomes from metagenomic samples. This is typically done using a combination of reference-based and de novo assembly approaches. Assembling the genomes from the metagenomic sample, prior to classification, could improve classification results and also aid in identifying new, previously unknown species. However, the evaluation of metagenome assemblies is a challenging task and it is important to assess the quality of the assemblies in order to ensure the accuracy of downstream analyses. In this paper, we provide a detailed overview of metagenomic classification, de novo metagenome assembly process, and evaluation of metagenome assembly, highlighting various tools and techniques currently available for each step. We also present initial results showing that metagenomic classification can benefit from a previously assembled metagenome.