apcamargo
commented
2 months ago Hi @Kir283,
You can identify these regions by looking for chains of multiple plasmid markers (GENOMAD.*.P*) uninterrupted by chromosome-specific markers (GENOMAD.*.C*) in the <prefix>_annotate/<prefix>_genes.tsv file. However, since conjugative elements can integrate into the chromosome, the presence of integrated plasmids shouldn't necessarily be a concern unless you have specific reasons to suspect this type of assembly error.
Is there any possibility to identify plasmids in the main contig so even if it's labelled as chromosome? I need to evaluate the correctness of different assemblies and would therefore like to determine whether plasmids have been incorrectly inserted into the chromosome by the assembler. Thank you in advance!