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Old 11-22-2010, 12:56 AM   #1
Autotroph
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Location: Europe

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Default Meta assembly

Hi,

I want to do a meta assembly using contigs generated from 8 different locations for the same organism(same technology-Illumina reads).

How should i proceed? Should i just run an assembly using all the 8 datasets as reads? How about using alignment tools for doing this?

Thanks
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Old 04-05-2012, 12:32 PM   #2
seb567
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Default

Hello,

Quote:
Originally Posted by Autotroph View Post
Hi,

I want to do a meta assembly using contigs generated from 8 different locations for the same organism(same technology-Illumina reads).
You can proceed with 8 separate de novo assemblies.



We use Ray to assemble gut microbiomes and it works well.


How to use Ray:

HTML Code:
mpiexec -n 64 Ray \
 -k \
 31 \
 -p \
 Sample/ERR011142_1.fastq.gz \
 Sample/ERR011142_2.fastq.gz \
 -p \
 Sample/ERR011143_1.fastq.gz \
 Sample/ERR011143_2.fastq.gz \
 -o \
 Assembly


Quote:
Originally Posted by Autotroph View Post
Hi,

How should i proceed? Should i just run an assembly using all the 8 datasets as reads? How about using alignment tools for doing this?

Thanks

There is many ways to go where you want to go.

You can read these two large-scale papers to see how they did it.

Nature 464, 59-65 (4 March 2010)


Nature 473, 174–180 (12 May 2011)



Obviously there are other approaches too should you choose the path of literature survey.


Good luck with this endeavor.


Sébastien Boisvert
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