degenerate nucleotide in abyss assemblies?

Question

[vtefnfqp]

Hi, everyone! I assembled a fungal genome using abyss-pe (ABySS, version 1.9.0). I notice that there are some degenerate nucleotides in the resulted scaffolds, e.g. [RYKM]. I read the readme file carefully but cannot find which parameter is about this.

Does anyone know how to turn off the degenerate nucleotides? Thank you very much!

Answer 1

[Shaun Jackman]

PathConsensus outputs the IUPAC ambiguity codes. Set either a=1 or p=1 to disable PathConsensus ambiguity codes. Note that this will also disable PopBubbles. You may prefer to simply replace ambiguity codes with an ACGT nucleotide or N after assembly, as Ben suggested.

See https://github.com/bcgsc/abyss/blob/master/bin/abyss-pe#L264-L267

[wjidea]

What is the consequence to not have the PopBubbles step then?

Answer 2

[benv]

Unfortunately, I don't think there is an ABySS option to turn off degenerate nucleotides. (I just did a grep through the source code to make sure.)

If the ambiguity codes are causing problems in downstream tools, you will have to "flatten" the bases as a post-processing step after assembly. The unix 'tr' program might be helpful for that.

[vtefnfqp]

Thanks! I replace the degenerate nucleotides as "N", and then the replaced "Ns" can be replaced by "ATCG" in the gapfilling step.