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Old 03-09-2011, 12:59 PM   #1
fenix
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Default Degenerate nucleotide mappers

Hi all,

I haven't exhaustively searched the literature, but to the best of my knowledge there aren't mapping tools that support degenerate nucleotides in their references (e.g., H = A or C or T) are there? Thanks in advance for your comments.

-Matt
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Old 03-09-2011, 04:50 PM   #2
n00c
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Mosaik supports IUPAC codes during alignment phase, but I don't know whether it uses them during the actual mapping.
http://bioinformatics.bc.edu/marthlab/Mosaik
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Old 03-09-2011, 07:04 PM   #3
sparks
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Novoalign also supports IUPAC codes in the reference and in the reads.

www.novocraft.com
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