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Old 09-10-2012, 05:57 PM   #1
jojohan
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Location: sun-yat-san university

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Lightbulb question about multiple K-mer use of velvet?

I have about 100G metagenomic raw data sequenced by Illumina paired-end Hiseq2000. I meant to assemble the raw data by velvet. But there exists a big problem for me to assemble them at one time, while if I split the big file into several small parts and assemble them respectively, I maybe lost part of the data. So I am wondering If I could use several different K-mers to velvet the raw data separately and emerge all the results to assemble again?
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Old 09-12-2012, 11:04 AM   #2
cliffbeall
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C. Titus Brown and group at Michigan State have some methods for normalizing and partitioning metagenomic data before running velvet that you might want to look at:
http://khmer.readthedocs.org/en/latest/index.html
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Old 09-12-2012, 05:02 PM   #3
jojohan
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thanks for your reply!
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