Good Morning Everyone,
So I have a small viral data set that I want to make a draft genome for comparisons to some other field isolates. We have a Torrent so all this data is single unpaired data. However there is an excellent reference for this virus so I was trying a reference based assembly with TMAP (v4.6) and it looks pretty good. I still had some gaps so I also did a de novo assembly using SPAdes(v3.5) which returned 205 contigs that I used TMAP map4 (BWA fastmap variant) which returns almost no coverage. Hopefully the picture attached will show this. The top is the mapped contigs to the reference and the bottom is the reference guided assembly.
I understand that I should see some differeance in these two paths but I feel that they should have been closer to each other than they are.
How do I tell which is the correct answer from this data set?