Can LastZ aligner work with IUPAC ambiguity in Fasta files?

Question

[Michael]

Hi,

I am trying to compare different tools to align contigs to our reference assembly. The reference contains IUPAC ambiguity codes. LastZ doesn't seem to handle them with the default settings:

lastz  ../../lsalmonis/LSalAtl2s.fasta[multiple] GCA_001005205.1_lsal_atl_canada_female_v1_genomic.fna  --notransition --step=20 --nogapped --format=sam 
FAILURE: bad fasta character in LSalAtl2s.fasta, >LSalAtl2s1: W

LastZ has the 'quantum DNA' feature, that lets one align strings over arbitrary alphabets, but that requires to define a new substitution matrix. I am uncertain if this is the right way to do this.

[Rohit]

I generally use the option --ambiguous=iupac in these cases

[GenoMax]

@Michael: Email Bob Harris (email can be found on this page), the author of lastz. He is good about responding to lastz queries.