Commit 7bdf8b96 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/algo.org: add Demo-X5 as the first example

parent a1c70cd9
......@@ -711,10 +711,19 @@ require either the =-g germline/homo-sapiens-g:IGH= option, or the multi-germlin
** Basic usage: PCR-based datasets, with primers in the V(D)J regions (such as BIOMED-2 primers)
#+BEGIN_SRC sh
./vidjil-algo -c clones -g germline/homo-sapiens.g -2 -3 -r 1 demo/Demo-X5.fa
# Detect the locus for each read, cluster and report clones starting from the first read (-r 1).
# including unexpected recombinations (-2). Assign the V(D)J genes and try to detect the CDR3s (-3).
# Demo-X5 is a collection of sequences on all human locus, including some incomplete or unusual recombinations:
# IGH (VDJ, DJ), IGK (VJ, V-KDE, Intron-KDE), IGL, TRA, TRB (VJ, DJ), TRG and TRD (VDDJ, Dd2-Dd3, Vd-Ja).
#+END_SRC
#+BEGIN_SRC sh
./vidjil-algo -g germline/homo-sapiens.g:IGH -3 demo/Stanford_S22.fasta
# Cluster the reads into clones, based on windows overlapping IGH CDR3s.
# Assign the VDJ genes and try to detect the CDR3 of each clone.
# Cluster the reads and report the clones, based on windows overlapping IGH CDR3s.
# Assign the V(D)J genes and try to detect the CDR3 of each clone.
# Summary of clones is available both on stdout, in out/Stanford_S22.vdj.fa and in out/Stanford_S22.vidjil.
#+END_SRC
......
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