Assessment of de novo genome assembly accuracy ?

Question

[Picasa]

Hi,

I would like to assess my de novo genome assembly. I only know REAPR (http://www.sanger.ac.uk/science/tools/reapr) but apparently it cannot be use if I have assembled my genome with multi libraries (different insert sizes).

Do you know any other software that can evaluate a de novo assembly ?

[Anand Rao]

Picasa - Were you able to successfully use REAPR for your analyses? I am trying to use REAPR to assess de novo assembly correctness, but am encountering some rather strange errors/warnings results, hence this question. Thanks!

Answer 1

[Brian Bushnell]

ALE: assembly likelihood estimator was designed for that purpose. Quast is also useful.

[Picasa]

Quast need a reference genome right ?

[Brian Bushnell]

Quast can use a reference, but it does not need a reference. Without a reference it cannot report a lot of the statistics like indel rate and misassemblies, but it's still useful for other statistics.