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Old 11-26-2014, 10:53 AM   #1
thebutcher
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Default Validating genome assembly

Hi,

I'm quite new to bioinformatics, so please excuse the simplicity of this post.

I've sequenced a fungal genome (<40 Mbp) using the Ion Torrent platform. I created a fragment library, which means that I should now have single end reads (right?)

MIRA seemed like a good choice of assembler so I used that as well as CLC to assemble the reads into contigs, but now I'm stuck. I'd like to compare the qualities of the MIRA and CLC assemblies using CGAL, but I have no idea how to use the program.

I've read the CGAL paper, but I'm not sure where to begin running this program on the cluster at my school and I can't find much info on this program anywhere else. Does anyone have any experience/suggestions as to how I should proceed?

Thanks in advance!
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Old 11-26-2014, 11:06 AM   #2
Brian Bushnell
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I like to run Quast for evaluating assemblies, and it's pretty easy to use. It's best if you have a reference but does not require one.
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Old 11-26-2014, 11:20 AM   #3
GenoMax
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Downloading CGAL and trying it out yourself may be the only option. There is no online help documentation (or so it appears). Hopefully there is help documentation included in the source code download.

You are going to need to do some leg work to find out how to run software on your local cluster (every site has different setup, local restrictions, best practices etc). If you run into specific issues, we can try to help.

Quast (that Brian already mentioned) has help documentation that you can look at.
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Old 11-26-2014, 02:40 PM   #4
thebutcher
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Thanks a lot! I will take a look at Quast. I downloaded CGAL and tried unzipping it in the cluster, but to no avail. It is a .tar file so I typed the command:

tar -xzvf file.tar

After that the command prompt disappeared and nothing else happened. Any ideas?
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