I have some WGS data from a bacterial isolate I am trying to analyze. I am struggling with some of the terminology so forgive any misuse please, but I have been trying to align my dataset, which I have quality-filtered, trimmed and assembled into contigs, with published genomes of the same organism (downloaded from GenBank as fna.gz files).
When using progressiveMauve through the usegalaxy webtool, I am getting 0 alignments. I originally tried this with just a fasta file from my isolate and the ATCC type strain but then included all other published genomes (8 in total) and still got 0 alignments. This has been with default settings.
Do you have any ideas why this isn't generating any alignment?