I'm new here and I'm hoping you may have some insights into my problem (I'm sorry in advance if this is a silly question, but I'm new to bioinformatics in general).
My overall goal is to align my whole genome sequence data using plasmidSPAdes to generate plasmid contigs (I'm only interested in the plasmid sequences for later analysis) and then put those together and complete gene predictions on the plasmids.
At this point, I have used plasmidSPAdes and have a .fasta file with my contigs, as well as a .fastg file that I've opened with Bandage, which seems to give me a very rudimentary map. Maybe I am overthinking it (maybe I already have all of the data/results and just need to open it) but I'm wondering if you may have suggestions as to how to put these contigs together (or at least try to) from the .fasta files so I can see the whole map for each plasmid? I've seen some programs (like Recycler, for example) that seem to do what I want, but I don't use Python and I'm not sure if it's possible to do with another program using what I already am (I'm using a Unix Shell -MobaXterm, but as far as I know, it's just using a normal command line, not Python, like Recycler requires - again, I apologize if I'm not explaining very well). I'm willing to learn Python if all else fails, but I'm only interested in using, say, Recycler for one stage overall and am hoping there's a way to do what I need without having to figure out a new program in a new system. Any input you might have would be greatly appreciated!