I'm back again to grovel at the feet of crowdsourced guidance. So far this is my workflow using ion torrent data to assemble viral genomes.
Torrent reads --> fastqc [Q20 or higher for 95% of the read] --> khmer [normalized to 20x] --> Mira [mostly default setting] --> Gap5 [for looking, and right now manual closure] --> MUMmer [promer, for contig alignment to close ref]
Then I use the MUMmer information to manually close the contigs. However I feel like there should be a way to use the alignment information generated by MUMmer to automate the mapping and closing but I'm sure how. I have not found a way to do this in the MUMmer documentation, but there should be a way. They give you all the coordinate data, so I should be able to take that information to make a draft genome. Right?
So my question is, is this possible to do and am I on the right track?
Thanks for any and all insight!