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`
nor on the standard output. They instead add a `clusters` sections in the `.vidjil` file
that will be visualized in the web application.
The `-n` 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
The `--cluster-epsilon` option triggers an automatic clustering using DBSCAN algorithm (Ester and al., 1996).
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
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
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
## Advanced usage
``` 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)
# 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')
# and can been seen and edited in the web application.
```
......
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