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Assigning V, D, J and C to nanopore sequence

Hi,

My aim is to carry out the following:

  1. Homology analysis of consensus sequences (nanopore platform, human) to TCR sequence reference databases and then assign the V, D, J, and C to individual sequences.

  2. Next, obtain the following table:

    TRAV TRJ CDR3 Reads %Reads

    TRAV25 TRJ36 CPRKSQTGAANLFF 543 0.44

    TRAV12-1 TRJ11 CVVNEGYSTLF 414 0.33

What is the best approach and what are the best tools?

Thanks in advance

nanopore repertoire annotation sequence tcr
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updated by colindaven colindaven • written by robjohn70000 robjohn70000

1 answer

I haven't had experience of this personally but here is a great list of tools and resources:

https://github.com/slowkow/awesome-vdj

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written by colindaven colindaven

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