Commit 6bbe5553 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/algo.org: stress that -3 requires gapped sequences

See #2187.
parent c1276675
......@@ -410,7 +410,10 @@ All the reads with the windows related to the sequence will be extracted to =out
The =-3= option launches a CDR3/JUNCTION detection based on the position
of Cys104 and Phe118/Trp118 amino acids. This detection relies on alignment
with gapped V and J sequences, as for instance, for V genes, IMGT/GENE-DB sequences.
with gapped V and J sequences, as for instance, for V genes, IMGT/GENE-DB sequences,
as provided by =make germline=.
The CDR3/JUNCTION detection won't work with custom non-gapped V/J repertoires.
CDR3 are reported as productive when they come from an in-frame recombination
and when the sequence does not contain any in-frame stop codons.
......
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