Assigning V, D, J and C to nanopore sequence

Question

[robjohn70000]

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

Answer 1

[colindaven]

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

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