Associate bio sample names with barcode pairs

If you want to assign a bio sample name with a barcode pair, you can use the SMRT Link feature or directly use it in lima version 2.2.0 or later.

For this, please create a CSV file with two columns Barcodes,Bio Sample. The first column contains the barcode names of the pair; if asymmetric is used, only give the pair a single name as the order of the barcodes in a pair is not relevant. Example:

Barcodes,Bio Sample
bc1001--bc1001,Alfred
bc1002--bc1002,Berthold
bc1003--bc1003,Constantin
bc1008--bc1008,Holger

Provide this CSV to lima via --biosample-csv input.csv.

This will associate the bio sample name to the read group using the SM tag.

UUID passthrough

Since lima v2.5.0, the functionality has been enhanced to allow specifying UUIDs for the resulting XML files; for this, use --reuse-uuids in addition to the extended csv for --biosample-csv. Example:

Barcodes,UUID,Bio Sample
bc1001--bc1001,11111111-1111-1aaa-0111-111111111111,Alfred
bc1002--bc1002,22222222-2222-2bbb-8222-222222222222,Berthold
bc1003--bc1003,33333333-3333-3ccc-9222-333333333333,Constantin
bc1008--bc1008,e04f12c9-7b2e-45fd-ab49-1bc2f75d653a,Holger

Ensure that the UUID matches the regex

[0-9a-f]{8}-[0-9a-f]{4}-[0-5][0-9a-f]{3}-[089ab][0-9a-f]{3}-[0-9a-f]{12}

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