So I'm using a local tool to annotate several relevant k-mer contigs. It uses both Fasta and GFF from Human Genome Reference assembly 38, and it's working fine and smoothly.
The only problem is a small part of my contigs align to more than one position on the Genome, and the tool is only able to display the information of one alignment. And I'm interested in any of the possible alignment, as the first one (which is displayed) isn't always the most relevant.
Are you guys aware of any annotation tool that I could use to align all of my "more than one hit" contigs and get the information on every single alignment ?
Thank you !