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2 changes: 1 addition & 1 deletion pipeline/README.md
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2. makeblastdb tool
3. MakeDb tool
4. R and the following R packages: seqinr, tigger, optparse, gtools, ggplot2, stringr, dplyr, data.table, alakazam, and reshape2
5. The fasta file refernces of the 3 segments: TRBV, TRBD, and TRBJ in IMGT format (gapped sequences). (the references can be found in the "Script_references" folder)
5. The fasta file refernces of the 3 segments: TRBV, TRBD, and TRBJ in IMGT format (gapped sequences). (the references can be found in the "fasta_references" folder)
6. Blast databases for germline TRBV, TRBD, and TRBJ sequences as describde over IgBlast set up: https://ncbi.github.io/igblast/cook/How-to-set-up.html (the references can be found in the "makeblastdb_references" folder)

## Initialize
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