Commit 0a91cec7 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/vidjil-algo.md: AIRR and -c

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......@@ -636,9 +636,10 @@ For example `-uu -X 1000` splits the unsegmented reads from the 1000 first reads
Since version 2018.10, vidjil-algo supports the [AIRR format](http://docs.airr-community.org/en/latest/datarep/rearrangements.html#fields).
We export all required fields, some optional fields, as also some custom fields (+).
Note that Vidjil-algo is designed to efficiently gather reads into clones. We thus report in the AIRR format *clones*.
Note that Vidjil-algo is designed to efficiently gather reads from large datasets into clones.
By default (`-c clones`), we thus report in the AIRR format *clones*.
See also [What is a clone ?](vidjil-format/#what-is-a-clone).
Using `-c segment` trigger a separate analysis for each read, but this is usually not advised for large datasets.
| Name | Type | AIRR 1.2 Description <br /> *vidjil-algo implementation* |
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