edamame-course / 2015-tutorials Goto Github PK

Hi all,

By chance I found this series of tutorials and was happy to see that you choose MEGAHIT in the assembly tutorial. Here I have some suggestions for the tutorial.

First the stat in tail of the log file is not for the whole assembled contigs. Many standalone contigs generated in previous iterations will not pass to the subsequent iterations, so the tail of the log only shows the contigs assembled for the last iteration. To calculate assembly stat, I suggest using other tools, say QUAST.

Second, we've just updated MEGAHIT to v0.3-b2, in which the PE info can be used and parameters -l is no longer needed. This tutorial uses v0.2.1, so I suggest amending the link in the tutorial to https://github.com/voutcn/megahit/tree/v0.2.1-a.

Cheers,
Dinghua