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Old 04-08-2014, 01:09 PM   #1
vanillasky
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Location: Europe

Join Date: Mar 2014
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Default Metavelvet-Evaluating an assembly

I started using MetaVelvet and have the following questions:

1. What percentage of a metagenome can one expect to assemble using this assembler for example? (and I mean using real metagenomic data as an example)

2. How do you access if the assembly is any good?

For my first test run I tried running the default parameters and noticed, compared to just velvet, I ended up with a high number of contigs, which makes sense since Metavelvet includes multiple coverages vs velvet. On the other hand the n50 did not differ much from Velvet and the size of the reads that make up the contigs doesn't vary much either (~100bp or smaller). I'm working with a marine metagenome with an input of about 2 million reads.
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