Hi,
I have an RNAseq data from TCR  alpha and bed chain single cell sequencing which I am trying to analyze.  I looked at the post https://www.biostars.org/p/148371/ and also read the Mark Davis paper and the protocol, which I thought would be appropriate to follow.  But I cannot either find the dataset from the Mark Davis paper not the tool they used (vdjfasta).  I was writing to ask what is the latest tool that would be appropriate for assembling the reads and getting a summary the TCR clones from my dataset.
Thanks,
- Pankaj
Software for T/B-cell receptor repertoire analysis using non-amplicon samples:

1. [TraCeR](https://github.com/Teichlab/tracer) T-cell receptors, single-cell RNA-Seq 
2. [VDjer](https://github.com/mozack/vdjer) B-cell receptors, RNA-Seq 

P.S. Check out [T cell fate and clonality inference from single-cell transcriptomes (Nature Methods 2016)](http://www.nature.com/nmeth/journal/v13/n4/full/nmeth.3800.html) that describes your case.