We did a metagenome sequencing on ONT and ran metaFlye to obtain contigs and polished with medaka. Out of the 318 contigs, around 21 contigs were prokaryotic contigs, and two of the contigs had 16S rRNA sequences annotated which we used for taxonomic classification, and it is a bacterium that our lab wants to target for further analysis.
Using BUSCO with the appropriate dataset based on the initial taxonomic classification, we see that three out of the 21 contigs had BUSCO orthologs. The BUSCO score of the three contigs as a single file is between 80 and 90%.
My first thought was to map the raw reads to the three contigs and reassemble the mapped using Flye without the
--meta option. Around 200,000 reads (750 Mb) of the initial 3 million reads were mapped and reassembled but it produced 51 contigs which leads me to believe that the three contigs were not the full sequences.
We also have a Illumina-assembled binned contig file (but not the raw reads). I want to ask there is a way to obtain a high quality draft genome of the target bacterium from ONT metagenome sequencing data. The BLAST searching the 16S rRNA showed a matches but the pairwise identity is 96.7% at the highest.
Thank you in advance.