Clonotype extraction can be performed using MiXCR. The pipeline includes alignment of raw sequencing reads using align, error correction and UMI grouping using correctAndSortTags, assembly of aligned sequences into clonotypes using assemble, and exporting the resulting clonotypes into tab-delimited file using exportClones.
The pattern used to detect UMI is:
^(R1:*)\^(UMI:N{18})(R2:*)
More details can be found on MiXCR official website (https://docs.milaboratories.com/).
Last modified:
29 September 2023
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