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gear-genomics / pearl

Patching references via trace assemblies
https://www.gear-genomics.com/pearl/
GNU General Public License v3.0
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Reference sequence can't contain degenerate/heterozygous bases #26

Open zygoballus opened 1 year ago

zygoballus commented 1 year ago

If the reference sequence contains a degenerate/heterozygous base (W, S, M, K, R, Y, etc.), it gives the error "FASTA file contains nucleotides != [ACGTN]."

As a quick and dirty fix, it could map these bases to N. The best fix would be to use the bases according to their meaning, e.g. C or T for Y.

untergasser commented 1 year ago

Yes, your quick fix is the intended way to use Pearl. The tool should be used to confirm nucleotide sequences, so degenerate/heterozygous bases will not solve the sequence.

Best, Andreas