Commit 8f1d824f authored by Mathieu Giraud's avatar Mathieu Giraud

doc/vidjil-algo.md: update

See #3295.
parent 2900822b
...@@ -477,11 +477,11 @@ The following options are experimental and have no consequences on the `.vdj.fa` ...@@ -477,11 +477,11 @@ The following options are experimental and have no consequences on the `.vdj.fa`
nor on the standard output. They instead add a `clusters` sections in the `.vidjil` file nor on the standard output. They instead add a `clusters` sections in the `.vidjil` file
that will be visualized in the web application. that will be visualized in the web application.
The `-n` option triggers an automatic clustering using DBSCAN algorithm (Ester and al., 1996). The `--cluster-epsilon` option triggers an automatic clustering using DBSCAN algorithm (Ester and al., 1996).
Using `-n 5` usually cluster reads within a distance of 1 mismatch (default score Using `--cluster-epsilon 5` usually cluster reads within a distance of 1 mismatch (default score
being +1 for a match and -4 for a mismatch). However, more distant reads can also being +1 for a match and -4 for a mismatch). However, more distant reads can also
be clustered when there are more than 10 reads within the distance threshold. be clustered when there are more than 10 reads within the distance threshold.
This behaviour can be controlled with the `-N` option. This behaviour can be controlled with the `-cluster-N` option.
The `-=` option allows to specify a file for manually clustering two windows The `-=` option allows to specify a file for manually clustering two windows
considered as similar. Such a file may be automatically produced by vidjil considered as similar. Such a file may be automatically produced by vidjil
...@@ -796,10 +796,10 @@ This file will be relatively small (a few kB or MB) and can be taken again as an ...@@ -796,10 +796,10 @@ This file will be relatively small (a few kB or MB) and can be taken again as an
## Advanced usage ## Advanced usage
``` bash ``` bash
./vidjil-algo -c clones -g germline/homo-sapiens.g -r 1 -n 5 -x 10000 demo/LIL-L4.fastq.gz ./vidjil-algo -c clones -g germline/homo-sapiens.g -r 1 --cluster-epsilon 5 -x 10000 demo/LIL-L4.fastq.gz
# Extracts the windows with at least 1 read each (-r 1, the default being -r 5) # Extracts the windows with at least 1 read each (-r 1, the default being -r 5)
# on the first 10,000 reads, then cluster them into clones # on the first 10,000 reads, then cluster them into clones
# with a second clustering step at distance five (-n 5) # with a second clustering step at distance five (--cluster-epsilon 5)
# The result of this second is in the .vidjil file ('clusters') # The result of this second is in the .vidjil file ('clusters')
# and can been seen and edited in the web application. # and can been seen and edited in the web application.
``` ```
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