Do you think it is useful to add an option that users can combine the scaffolds and the unplaced contigs into a single fasta file instead of two separate files? Because I think the unplaced contigs are also useful for downstream analysis.
Combining these two outputs is a simple cat operation - I don't think there should be an extra option for that. Logically the contents of two files is very different.
Do you think it is useful to add an option that users can combine the scaffolds and the unplaced contigs into a single fasta file instead of two separate files? Because I think the unplaced contigs are also useful for downstream analysis.