Commit c7d506e7 authored by Mathieu Giraud's avatar Mathieu Giraud Committed by Mikael Salson

doc/algo.org: documents -Z

parent ba3aa473
...@@ -388,8 +388,8 @@ to display the clones on the grid (otherwise they are displayed on the ...@@ -388,8 +388,8 @@ to display the clones on the grid (otherwise they are displayed on the
If you want to analyze more clones, you should use =-z 200= or If you want to analyze more clones, you should use =-z 200= or
=-z 500=. It is not recommended to use larger values: outputting more =-z 500=. It is not recommended to use larger values: outputting more
than 500 clones is often not useful since they can not be visualized easily than 500 clones is often not useful since they can not be visualized easily
in the web application, and takes large computation time (full dynamic programming, in the web application, and takes large computation time (full dynamic programming
see below). with all germline sequences), possibly reduced when using =-Z= (see below).
Note that even if a clone is not in the top 100 (or 200, or 500) but Note that even if a clone is not in the top 100 (or 200, or 500) but
still passes the =-r=, =-%= options, it is still reported in both the =.vidjil= still passes the =-r=, =-%= options, it is still reported in both the =.vidjil=
...@@ -404,6 +404,12 @@ The =-A= option disables all these thresholds. This option should be ...@@ -404,6 +404,12 @@ The =-A= option disables all these thresholds. This option should be
used only for test and debug purposes, on very small datasets, and used only for test and debug purposes, on very small datasets, and
produce large file and takes huge computation times. produce large file and takes huge computation times.
The experimental =-Z= option speeds up the full analysis by a pre-processing step,
again based on k-mers, to select a subset of the V germline genes to be compared to the read.
The option gives the typical size of this subset (it can be larger when several V germlines
genes are very similar, or smaller when there are not enough V germline genes).
Setting =-Z 5= is generally safe. With the default option, =-Z all=, this
pre-processing step is not activated.
** Sequences of interest ** Sequences of interest
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