Handle trusted circular contigs

[fplazaonate]

Is your feature request related to a problem? Please describe. For generic questions use Q&A section in the Discussions forum above.

Hello,

I would like to perform hybrid metagenomic assembly combining Illumina and PacBio data.
I have generated a PacBio assembly with metaFlye. I would like to use it with the --trusted-contigs option. However, some contigs are circular but I don't know if SPAdes can take this information into account?

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Describe alternatives you've considered

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Additional context

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[asl]

Your contigs are still linear in the input file. However, if the ends would overlap by at least largest k-mer length, then it would help a bit.

[fplazaonate]

It seems that there is no overlap at the ends. Is there any way to provide a GFA graph as input?

[asl]

No

[fplazaonate]

Ok. I will compare the PacBio assembly with the hybrid assembly and make sure that changes introduced in circular contigs are only indels or substitutions corrections.