SQMtools: automated processing and visual analysis of ’omics data with R and anvi’o

摘要

Main workflow of the SQMtools pipeline. Raw reads are processed automatically by SqueezeMeta, which integrates assembly, ORF prediction, annotation and binning. The results can then be easily filtered and explored either with R (by creating a SQM object) or anvi’o (by creating an anvi’o database) in order to produce custom plots with the information of interest. Arrows correspond to function calls (e.g. going from raw reads to a krona chart would involve three function calls). The workflow is exemplified in detail in the Supplementary Information