High throughput sequencing platforms have revolutionized the detection and characterization of microbial species. Taxonomy classification is often greatly influenced by many parameters, from sample collection, DNA extraction, library preparation and data analysis. Among these, read length is one of the key parameters affecting the results. The popular Illumina sequencing platforms offer read length from 2x 50bp to 2x 300bp. For target-based metagenomic studies, the Illumina MiSeq platform has been widely used, whereas for shotgun metagenomic sequencing, the latest NovaSeq 6000 platform is more cost-effective.
At AGRF, microbial sequencing projects including amplicon and shotgun metagenomics include ZymoBIOMICS (D6311) as an internal control for evaluation of the sequencing run. The ZymoBIOMICS mock community is a mixture of genomic DNA from eight bacterial and two fungal strains. It was constructed by pooling predefined amount of DNA extracted from pure cultures of the ten microbial strains consisting of both Gram-negative and Gram-positive bacteria and yeast with varying sizes and cell wall compositions.
Many tools have been developed for detecting microbial taxonomy and estimating microbial abundance. In this study, we compare taxonomy classification performance of using the 2x 150bp and 2x 250bp NovaSeq reads from the ZymoBIOMICS controls on various taxonomy classifiers.