Commit 45e3bba4 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/algo.org: details

parent a1c41609
......@@ -296,7 +296,9 @@ Window prediction
-t <int> trim V and J genes (resp. 5' and 3' regions) to keep at most <int> nt (default: 0) (0: no trim)
#+END_EXAMPLE
The =-s=, =-k= are the options of the seed-based heuristic. A detailed
The =-s=, =-k= are the options of the seed-based heuristic that detects
"junctions", that is a zone in a read that is similar to V genes on its
left end and similar to J genes in its right end. A detailed
explanation can be found in (Giraud, Salson and al., 2014).
/These options are for advanced usage, the defaults values should work./
The =-s= or =-k= option selects the seed used for the k-mer V/J affectation.
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