Question: de novo workflow
0
gravatar for skbrimer
4.9 years ago by
skbrimer620
United States
skbrimer620 wrote:

Hi everyone, 

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!

Sean

sequencing alignment genome • 1.1k views
ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by skbrimer620
2
gravatar for skbrimer
4.9 years ago by
skbrimer620
United States
skbrimer620 wrote:

To answer my own question, and to help anyone else who may stumble down my road as well. The function I was looking for was in the show-tiling command. 

show-tiling -p <filename for output> <delta filing> 

Hope this helps anyone else. 

ADD COMMENTlink written 4.9 years ago by skbrimer620
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