ctb/khmer — Issue #9: what would it take to accept ambiguous nucleotides?
Author: leipzig
Created: 2012-02-23 16:13:42+00:00
State: open

Perhaps this was discussed during khmer's initial design, but i would like a version of khmer (khmer-rouge?) that would parse an "injected reference" containing the bi-ambiguous nucleotides R, W, Y, M, K, and S (http://www.vivo.colostate.edu/molkit/help.html)

So TTRCC kmer 4 is (TTGCC or TTACC): TTGC,TTAC,TGCC,TACC,GGCA,GCAA,GGTA,GTAA

Since these symbols would expand the number of distinct kmers found in exponentially, i think there could be some sane limit (e.g. one) to the number of ambiguous nucleotides the program would accept within a kmer window.

How difficult would this be to implement?