Hi, First of all, please check our new MiXCR 4 which has a dedicated support for Takara kits (including UMI support for kits with molecular barcodes).

e.g.

mixcr analyze takara-human-bcr-cdr3 \
  input_R1.fastq.gz \
  input_R2.fastq.gz \
  result 

More on that here: https://docs.milaboratories.com/mixcr/reference/overview-built-in-presets/#takara-bio

To answer your questions: 1) No, you dont need any additional preprocessing before MiXCR. Sometimes you can use some normalization after you get clonotype tables: to the number of reads or UMI for example. More on that here: https://docs.milaboratories.com/mixcr/reference/mixcr-downsample/

2) I would include both positive and negative controls to ensure that you negative control does not have any clones and positive control returns the expected result.

3) You can use MiXCR postanalysis directly to access clonality and diversity metrics. More on that here: https://docs.milaboratories.com/mixcr/reference/mixcr-postanalysis/#diversity-measures