QC my de novo assembly

[vallejov]

Hi all,

I would like to QC my de novo assembly by comparing it to an EST library (no genome sequence available) but I don't have a clue how to go about doing that! I would appreciate any and all suggestions for a methodology.

Thanks a bunch!!

[yzzhang]

I used sim4db and exonerate to align ESTs to my assembly. Sim4db worked well and quick for me. You also can use GMAP to do this. I remember there is a thread just talking about this issue in this forum, [URL="http://http://seqanswers.com/forums/showthread.php?t=11764&highlight=map+est+genome"]. You can get what you need.
Best,

[vallejov]

Thank you so much yzzhang! I tried installing sim4db but am having problems when I run the configuration.sh file. It says that it can't find the python headers (python.h). Did you encounter this problem too? I re-installed the development headers for my version of python (2.7.3) but that did not change anything. Thanks again for your suggestions, I'll keep trying to make sim4db work!

[yzzhang]

I just ran the command "gmake install", but did not do the configuration step. Sim4db works for me anyway. You can try to use it now