adadiehl
commented
2 months ago Solved my problem: due to a change in verbiage in the documentation rendering "query genome" as the reference genome, and target genome for what other tools call query genome, had the fasta files supplied in the wrong order.
I am not sure whether this is a bug or a feature, but in examining output of a trial of ragtag patch, I noticed that ragtag.patch.fasta contains the same number of sequences as the reference genome, suggesting that unplaced contigs from the query genome were not included in the output. If this is a feature, it would be useful to be able to override this behavior and include unplaced contigs in the output.