We've been using dragonflye for some hybrid assemblies recently and have noticed a few unexpected results when running mob-recon on the assemblies. In one example, mob-recon included a small (~2kb) contig into the chromosome, despite the assembly including a large circular contig that appeared to be a complete chromosome. It seemed that mob-recon should have recognized the chromosome as being complete/circularized, so it wouldn't make sense to include other contigs into the chromosome reconstruction.
I suspect the reason this is happening is that mob-recon looks for a unicycler-style circularization tag in the fasta headers, which looks like: circular=true. But dragonflye (and presumably flye itself, though I haven't confirmed) add a tag that looks like: circular=Y.
Am I understanding how mob-recon detects circular contigs correctly? Would it be straightforward to support both circular=true and circular=Y? If this isn't straightforward to do in mob-recon then we could make a little sed command that converts circular=Y to circular=true. But other users would need to do the same thing in all of their codebases too, so it seems like a less efficient solution.
We've been using dragonflye for some hybrid assemblies recently and have noticed a few unexpected results when running mob-recon on the assemblies. In one example, mob-recon included a small (~2kb) contig into the chromosome, despite the assembly including a large circular contig that appeared to be a complete chromosome. It seemed that mob-recon should have recognized the chromosome as being complete/circularized, so it wouldn't make sense to include other contigs into the chromosome reconstruction.
I suspect the reason this is happening is that mob-recon looks for a unicycler-style circularization tag in the fasta headers, which looks like:
circular=true. But dragonflye (and presumably flye itself, though I haven't confirmed) add a tag that looks like:circular=Y.Am I understanding how mob-recon detects circular contigs correctly? Would it be straightforward to support both
circular=trueandcircular=Y? If this isn't straightforward to do in mob-recon then we could make a little sed command that convertscircular=Ytocircular=true. But other users would need to do the same thing in all of their codebases too, so it seems like a less efficient solution.