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Commit a566dfdf authored by Mathieu Giraud's avatar Mathieu Giraud

doc/user.md: repertoire studies, reword summary and filter/top

parent c8c814bd
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......@@ -554,10 +554,13 @@ to see in itself. In a typical dataset with about 10<sup>6</sup> reads, even in
the presence of a dominant clone, there can be 10<sup>4</sup> or 10<sup>5</sup> different
clones detected. A dominant clone can have thousands or even more reads.
For most of the cases, one may want to focus on some clones with their consensus sequences,
Whereas many applications require to focus on some clones with their consensus sequences,
repertoire studies usually consider all clones,
for example to assess their diversity or to compare repertoires between samples.
Vidjil allows both:
- to fully study these "top clones"
- to study the distribution of the "smaller clones"
- to fully study some "top clones"
- to study the distribution of all the clones
- to estimate diversity and overlap indices
- when this is needed, to retrieve the full list of clones and/or reads
......@@ -589,12 +592,15 @@ It should then show up in any sample.
in the `.analysis` file, it will always be shown even if it does not
meet the "top" filter.
## Studying the distribution of "smaller clones"
## Studying the distribution of all clones, including "smaller clones"
Vidjil detects all clones, even if, by default,
only the top 50 or 100 clones are displayed with a full analysis.
The other clones, that are hidden (because of the "top" or because of hiding some tags)
are gathered into *virtual clones*, shown with light gray.
The top 50/top 100 clones are displayed but all of them are computed and are useful to study full repertoires,
This enables to study full repertoires,
including assessing the polyclonal background and the diversity of the repertoires.
Clones that are hidden (because of the "top" or because of hiding some tags)
are gathered into virtual clones, shown with light gray.
Note that selecting `color by clone` emphasizes the difference between the top clones, colored, and these virtual clones.
Depending on the process configuration, these "smaller clones" are shown, in the clone list:
......@@ -612,7 +618,7 @@ analyzed reads, including the hidden clones.
## Studying diversity and overlap indices
Several indices are computed to assess the diversity and overlap of sample(s):
Several indices are computed on the full list of clones to assess the diversity and overlap of sample(s):
- On one sample, [diversity indices](https://en.wikipedia.org/wiki/Diversity_index) such as
Shannon's diversity, Shannon's equitability and Simpson's diversity, as computed by [vijdil-algo](vidjil-algo.md#diversity-measures).
......
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