Fig. 1

Workflow chart for recovering mitochondrial genomes from metagenomic sequence datasets. The mitochondrion reference genome KP231180 was used twice to generate new assemblies using metagenomic reads from stool samples. First, NGS reads were mapped to the reference to gather mitochondrion-specific sequences. Secondly, after the assembly the orientation of the sequences in the new assemblies were corrected to be in alignment to the reference genome for downstream analysis. It is anticipated that the reference-guided, de novo assembly workflow can be modified to fit the nature of any NGS datasets