8.4. Alignment and clonotypes assembly using MiXCR

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:*)

You can use the following presets for the MiXCR analysis:

For the DriverMap AIR RNA Kit:
cellecta-human-rna-xcr-umi-drivermap-air

For the DriverMap AIR DNA Kit:
cellecta-human-dna-xcr-umi-drivermap-air

For the DriverMap AIR RNA Full-length Kit:
cellecta-human-rna-xcr-full-length-umi-drivermap-air

For the DriverMap AIR Mouse Kit:
cellecta-mouse-rna-xcr-umi-drivermap-air

More details can be found on the MiXCR official website: Cellecta AIR Assay Guide.