Hi all,
Has anyone had any issues with SPAdes outputting duplicate sequences between plasmid and chromosome assembly outputs? I have an assembly ready to submit to NCBI but they won't take it because of 74 instances of a contig being found in a plasmid that is also found in the chromosome.
I am going to be parsimonious in my assumption that this is a result of assembly and not perhaps recombination between the chromosome and the plasmid. I tried blasting the sequences that were marked as having a duplicate to see if they are more likely in other genomes of the same species to align to chromosome or plasmid sequence, but in many instances they could go either way (no overwhelming alignment to either chromosome or plasmid sequences in GenBank).
Has anyone else run into this issue before, specifically with SPAdes?
Thanks
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