General method for circularizing genomes from metagenomes.

(A) Reads have adapters trimmed and low-quality reads are filtered using BBtools. (B) Processed reads are assembled into contigs using SPAdes. (C) Contigs are grouped into bins using MetaBAT 2. (D) After choosing a bin for circularization, reads mapping to the bin are extracted from the original processed reads and used as input into (E) where they are assembled into contigs using MIRA. (F) Steps D and E are repeated as necessary until the bin is deemed to be in a Circularization, Idempotence, or Chaos state. (G) If a bin is deemed circular, we do final checks for misassemblies using Pilon and for the presence of rRNA, tRNAs, and RNase P RNA before officially calling the bin a circularized genome.