[mira_talk] Re: Need suggestion on quality of NGS data and post assembly procedures
- From: Chris Hoefler <hoeflerb@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Tue, 16 Jun 2015 09:18:40 -0500
Now I need any experienced person to suggest kindly that is it wise to
continue with this data? How hard it will be for me to complete this
project successfully. what are the best tools and methods I can use on this?
It depends a bit on what your goal is. What do you want to achieve with
this genome? I think it is safe to say you will not be able to get a
"finished" genome with this data. But there is still plenty of analysis you
can do with a draft or partially assembled genome. Is 3 Mb the expected
size of your genome? The combination of moderately high-GC with ion
torrent, which has homopolymer problems, is going to be bad for any genome
assembly effort. What options do you have to acquire more data?
On Tue, Jun 16, 2015 at 3:36 AM, Rameez Mj <rameez03online@xxxxxxxxx> wrote:
I have a bacterial whole genome project going on with iontorrent proton
200bp platform. I analysed my data with princeq. It being of high average
coverage suggested by MIRA(129x). I removed exact duplicates with
princess-lite and extracted 1800000 reads randomly using a python script
"subsampler". MIRA assembles it to >3000 contigs (details are there in the
assembly log).Result of data analysis using princess, Assembly log and
result info generated by MIRA is attached.
Now I need any experienced person to suggest kindly that is it wise to
continue with this data? How hard it will be for me to complete this
project successfully. what are the best tools and methods I can use on
this?
I know the question is raw but I expect something from you.Thanking you in
advance.
--
Chris Hoefler, PhD
Postdoctoral Research Associate
Straight Lab
Texas A&M University
2128 TAMU
College Station, TX 77843-2128
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