Question: Assessment of de novo genome assembly accuracy ?
0
gravatar for Picasa
2.4 years ago by
Picasa390
Picasa390 wrote:

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 ?

genome accuracy • 950 views
ADD COMMENTlink modified 2.4 years ago by Brian Bushnell16k • written 2.4 years ago by Picasa390

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!

ADD REPLYlink modified 19 months ago • written 19 months ago by Anand Rao210
3
gravatar for Brian Bushnell
2.4 years ago by
Walnut Creek, USA
Brian Bushnell16k wrote:

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

ADD COMMENTlink written 2.4 years ago by Brian Bushnell16k

Quast need a reference genome right ?

ADD REPLYlink written 2.4 years ago by Picasa390

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.

ADD REPLYlink written 2.4 years ago by Brian Bushnell16k
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