TAXAPRO: A Streamlined Pipeline to Analyze Shotgun Metagenomes

Background: The ability to promptly sequence whole genomes at a relatively low cost has revolutionized how we study the microbiome. Analyzing whole genome sequencing (WGS) data enables metagenomics at scale. Still, it is a complex process that involves multiple moving parts and can be unintuitive for scientists that do not typically work with this type of data. Methods: Thus, to help lower the barrier for less computationally inclined individuals, TAXAPRO, a metagenomics pipeline that accurately assembles organelle genomes from WGS, data was developed. TAXAPRO seamlessly combines WGS analysis tools to create a pipeline that automatically processes raw WGS data and presents information on microorganisms’ diversity and relative abundance. Results: TAXAPRO was evaluated using gut microbiome data from COVID-19 patients. Analysis performed by TAXAPRO demonstrated a relatively high abundance of Clostridia and Bacteroides genera and a low abundance of Proteobacteria were detected in the gut microbiome of patients hospitalized with COVID-19, consistent with the original findings results derived using a different analysis methodology. Conclusion: Our results provide evidence that the TAXAPRO workflow dispenses quick and automated microorganism diversity and relative abundance information without the hassle of manually performing the analysis.