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Old 05-07-2014, 04:36 AM   #1
vanillasky
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Location: Europe

Join Date: Mar 2014
Posts: 42
Default velvetg stops due to memory shortage

Hi all,

I have tried to use the velvetg for my metagenomic data assembly steps prior to MetaVelvet.

My machine is about 250GiB RAM.

The read length is about 90 for my dataset. The total number reads is about 20 million for a combined and inverleaved fastq file.

However, when I try to run velvetg it it takes about two days before the program is killed.

Can anyone give me recommendations on how much to increase my RAM for such a dataset? I have set the Kmer to 13 for my dataset and have turned on scaffolding, automatic coverage and automatic expected coverage since this is a metagenome.
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