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Old 01-14-2015, 05:23 AM   #1
TauOvermind
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Default Which metagenome assemblers are capable of efficient running on clusters?

Hi, I am trying to choose a metagenome assembler that would be able to run efficiently on a cluster (utilising cores from different nodes and using shared memory). While there are many very good assemblers out there (IDBA-UD, SPAdes, Meta-Velvet), it seems that only Ray-Meta is able to run in parallel. Are there any alternatives to Ray-Meta, or should I just stick to it?
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Old 01-14-2015, 05:40 AM   #2
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Not really an answer to your question in any sense, but in my opinion the quality of the assembly is a thousand fold more important than how long it takes to make it.
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Old 01-14-2015, 06:03 AM   #3
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rhinoceros, I completely agree with your point. Although I spent 3 days last time waiting for IDBA-UD to finish running, I got quite good contigs in the end.
I just wanted to know if there is a way to decrease waiting time, so I turned to the use of cluster. As far as I understood, IDBA-UD was not capable of parallel computing, and I compared Ray-Meta output to IDBA-UD output. Unfortunately, it seems that IDBA-UD is a better option for the reads I have.
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