Commit b72c36a4 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/ productivity

See #1824.
parent cdbc80de
......@@ -402,6 +402,8 @@ 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.
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.
The advanced =-f= option sets the parameters used in the comparisons between
the clone sequence and the V(D)J germline genes. The default values should work.
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