Report common T-cell receptor sequences

[donkirkby]

After merging the reads and checking for the V3LOOP amplicon, check for T-cell receptor alpha and beta (TCA and TCB) matches. Take all of those matches, and report the most common nucleotide sequences, by exact match. For the first version, report any sequences with prevalence of at least 5% of all T-cell receptor matches.

[jeff-k]

This looks like it would be the way to generate v-quest style results offline: https://github.com/williamdlees/TRIgS/blob/master/docs/IgBLASTPlus.md

[jeff-k]

I followed a similar strategy to that in the script above, parsing the text output of NCBI's igblastn tool (https://ncbi.github.io/igblast/) which has been set up to match IMGT's v-quest tool with these references: http://www.imgt.org/IMGT_vquest/share/textes/datareleases.html

Note that igblast may be a suitable tool for an HLA pipeline.