Best tools for scTCR-seq (VDJ) analysis?

Question

[yueli7]

Hello,

I will analysis scTCR-seq datasets of single-cell immune receptor receptor.

Which one is the best tool for VDJ data analysis? VDJ tools, clonotypr, VDJServer, VDJML or scRepertoire?

Thanks in advance for great help!

Best Wishes,

Yue

[Friederike]

What types of question do you have?

[yueli7]

Hello Fridederike,

Thank you for your message. I want to ask which one it the best tools for analysis scTCR-seq data?

Thank you in advance for your great help!

Best,

Yue

[seidel]

Yue,

...best tools for analysis scTCR-seq data?

Analysis begins with questions, not tools. Friederike is asking, "what are the questions you are asking of your data?" so that we can then form ideas about what tools would best answer those questions.

[yueli7]

Hello Seidel,

Thank you for your message!

I made the change.

Thank you again!

Best,

Yue

Answer 1

[Ming Tommy Tang]

I have collected a bunch of tools at https://github.com/crazyhottommy/TCR-BCR-seq-analysis

Answer 2

[mizraelson]

Since series 4 MiXCR software supports single-cell. It is also very easy to use and it supports most of the commercial single cell protocols and can be customized.

https://docs.milaboratories.com/mixcr/reference/overview-built-in-presets/