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First run

The easiest way to run even a sophisticated upstream analysis pipeline is by a single MiXCR analyze command:

mixcr analyze \
      takara-human-bcr-full-length \
      sample_R1_L{{n}}.fastq.gz \
      sample_R2_L{{n}}.fastq.gz \
This example runs an optimized analysis pipeline for the full-length human BCR molecular-barcoded data, obtained with SMART-Seq Human BCR kit. Option takara-human-bcr-full-length corresponds to MiXCR preset for this particular wet lab protocol and {{n}} syntax is used to concatenate samples across multiple lanes.

MiXCR provides a comprehensive list of available presets for plenty of protocols, data types and commercially available kits. One can find optimized analysis workflows for the following suppliers:

Supplier Species Data types
MiLaboratories Homo Sapience, Mus Musculus, Monkey amplicon BCR, TCR
Takara Bio Homo Sapience, Mus Musculus amplicon BCR, TCR
10x Genomics any single-cell VDJ, 5' GEX
Illumina Homo Sapience amplicon TCR
Qiagen Homo Sapience, Mus Musculus amplicon TCR
iRepertoire Homo Sapience, Mus Musculus amplicon BCR, TCR
Thermo Fisher Homo Sapience amplicon BCR, TCR
AbHelix Homo Sapience amplicon TCR, BCR
BD Homo Sapience, Mus Musculus single-cell VDJ
Oxford Nanopore any long-read VDJ
ParseBio any single-cell 3' GEX
NEB Homo Sapience, Mus Musculus amplicon TCR, BCR

Also, there are dedicated presets for generic data types and open-source protocols, including:

The further details can be found in the following materials: