Scaffold evaluation measures

[ebioman]

Hello,

I want to compare the scaffolding of different assemblies and looking for good measures to evaluate the quality.

1. N 50
2. NG 50
3. Blastx and evaluate how many align
4. ...

Was my previous approach, now I am seeking new ones. The biggest obstacle using other methods of evaluation often is the lack of a reference genome in my case.

Any good suggestions ?

[flxlex]

Have a look here: http://flxlexblog.wordpress.com/2013...athon2-debate/. More are appearing in the literature all the time...