Commit 404dbc33 authored by Mathieu Giraud's avatar Mathieu Giraud

algo.org: help on -w

parent d23f26b0
......@@ -78,6 +78,36 @@ browser. They are intented for a command-line use only.
Launching vidjil with =-h= option provides the list of parameters that can be
used.
** Main algorithm parameters
#+BEGIN_EXAMPLE
Window prediction
(use either -s or -k option, but not both)
-s <string> spaced seed used for the V/J affectation
(default: #####-#####, ######-######, #######-#######, depends on germline)
-k <int> k-mer size used for the V/J affectation (default: 10, 12, 13, depends on germline)
(using -k option is equivalent to set with -s a contiguous seed with only '#' characters)
-w <int> w-mer size used for the length of the extracted window (default: 40)(default with -d: 60)
#+END_EXAMPLE
The =-s= and =-k= options are the options of the heuristic. A detailed
explanation can be found in the paper. More help on that will be
available in the following months. The defaults values should work.
The =-w= option fixes the size of the "window" that is the main
identifier to gather clones. The defaults values (40 for TRG, 60 for
IGH) were selected to ensure a high-quality clone gathering. The
high-throughput heuristic predicts the center of the "window" that may
shifted by a few bases from the actual "center" of the CDR3 (for TRG,
less than 15 bases compared to the IMGT/V-QUEST or IgBlast prediction
in >99% of cases). The extracted window should be large enough to
fully contain the CDR3 as well as some part of the end of the V and
the start of the J to uniquely identify a clone.
Setting =-w= to 30 for TRG and 50 for IGH may "segment" (analyze) a
few more reads, but may in some rare cases falsely cluster reads from
different clones. Setting =-w= to lower values is not recommended.
** Force to follow some sequences
Vidjil allows to specify a list of windows that must be followed
......
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