Commit 98ae7f83 authored by Mathieu Giraud's avatar Mathieu Giraud
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algo.org: update help

parent cbff91f3
......@@ -128,10 +128,9 @@ Germline databases (one -V/(-D)/-J, or -G, or -g option must be given for all co
-g <path> multiple germlines (in the path <path>, takes TRA, TRB, TRG, TRD, IGH and IGL and sets window prediction parameters)
#+END_EXAMPLE
There are three different ways
- Options such as =-G germline/IGH= or =-G germline/TRG= select one germline system.
- The =-V/(-D)/-J= options enable to select individual V, (D) and J repertoires (fasta files).
This allows in particular to select incomplete rearrangement using V or J repertoires.
This allows in particular to select incomplete rearrangement using custom V or J repertoires with added sequences.
- The =-g germline/= option launches the analysis on the six germlines (TRG and IGH are tested first, then the other ones).
Now the seed and window parameters are hard-coded for each germline. In a future release, the mechanism will be more flexible
and will parse the =germline/germlines.data= file.
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