In my last post, I described what a De Bruijn Graph assembler is and will now go into a short tutorial of how to begin using MetaVelvet.  MetaVelvet is an extension of the popular single genome De Bruijn Graph assembler, Velvet, and is optimized to handle the varying coverage and diversity of genomes in metagenomic samples and is executed through 3 steps: velveth, velvetg, and meta-velvetg.

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Calculate the N50 of Assembled Contigs

The N50 is metric that is often associated with the length of contigs post-assembly.  In my mind, I find it best to think of it as a weighted median where longer contigs are given a greater weight.   The N50 is defined as follows: Continue reading