├── .gitignore ├── Dockerfile ├── LICENSE ├── README.md ├── docker_wrapper.sh ├── gencode_parse.py ├── requirements.txt ├── resources ├── Hsap │ ├── colours.csv │ ├── combinatorial_recombinomes │ │ ├── TCR_A.1.bt2 │ │ ├── TCR_A.2.bt2 │ │ ├── TCR_A.3.bt2 │ │ ├── TCR_A.4.bt2 │ │ ├── TCR_A.fa │ │ ├── TCR_A.rev.1.bt2 │ │ ├── TCR_A.rev.2.bt2 │ │ ├── TCR_B.1.bt2 │ │ ├── TCR_B.2.bt2 │ │ ├── TCR_B.3.bt2 │ │ ├── TCR_B.4.bt2 │ │ ├── TCR_B.fa │ │ ├── TCR_B.rev.1.bt2 │ │ ├── TCR_B.rev.2.bt2 │ │ ├── TCR_D.1.bt2 │ │ ├── TCR_D.2.bt2 │ │ ├── TCR_D.3.bt2 │ │ ├── TCR_D.4.bt2 │ │ ├── TCR_D.fa │ │ ├── TCR_D.rev.1.bt2 │ │ ├── TCR_D.rev.2.bt2 │ │ ├── TCR_G.1.bt2 │ │ ├── TCR_G.2.bt2 │ │ ├── TCR_G.3.bt2 │ │ ├── TCR_G.4.bt2 │ │ ├── TCR_G.fa │ │ ├── TCR_G.rev.1.bt2 │ │ └── TCR_G.rev.2.bt2 │ ├── igblast_dbs │ │ ├── TCR_D.fa │ │ ├── TCR_D.fa.nhr │ │ ├── TCR_D.fa.nin │ │ ├── TCR_D.fa.nog │ │ ├── TCR_D.fa.nsd │ │ ├── TCR_D.fa.nsi │ │ ├── TCR_D.fa.nsq │ │ ├── TCR_J.fa │ │ ├── TCR_J.fa.nhr │ │ ├── TCR_J.fa.nin │ │ ├── TCR_J.fa.nog │ │ ├── TCR_J.fa.nsd │ │ ├── TCR_J.fa.nsi │ │ ├── TCR_J.fa.nsq │ │ ├── TCR_V.fa │ │ ├── TCR_V.fa.nhr │ │ ├── TCR_V.fa.nin │ │ ├── TCR_V.fa.nog │ │ ├── TCR_V.fa.nsd │ │ ├── TCR_V.fa.nsi │ │ └── TCR_V.fa.nsq │ ├── invariant_cells.json │ └── raw_seqs │ │ ├── TCR_A_C.fa │ │ ├── TCR_A_J.fa │ │ ├── TCR_A_V.fa │ │ ├── TCR_B_C.fa │ │ ├── TCR_B_D.fa │ │ ├── TCR_B_J.fa │ │ ├── TCR_B_V.fa │ │ ├── TCR_D_C.fa │ │ ├── TCR_D_D.fa │ │ ├── TCR_D_J.fa │ │ ├── TCR_D_V.fa │ │ ├── TCR_G_C.fa │ │ ├── TCR_G_J.fa │ │ └── TCR_G_V.fa └── Mmus │ ├── colours.csv │ ├── combinatorial_recombinomes │ ├── TCR_A.1.bt2 │ ├── TCR_A.2.bt2 │ ├── TCR_A.3.bt2 │ ├── TCR_A.4.bt2 │ ├── TCR_A.fa │ ├── TCR_A.rev.1.bt2 │ ├── TCR_A.rev.2.bt2 │ ├── TCR_B.1.bt2 │ ├── TCR_B.2.bt2 │ ├── TCR_B.3.bt2 │ ├── TCR_B.4.bt2 │ ├── TCR_B.fa │ ├── TCR_B.rev.1.bt2 │ ├── TCR_B.rev.2.bt2 │ ├── TCR_D.1.bt2 │ ├── TCR_D.2.bt2 │ ├── TCR_D.3.bt2 │ ├── TCR_D.4.bt2 │ ├── TCR_D.fa │ ├── TCR_D.rev.1.bt2 │ ├── TCR_D.rev.2.bt2 │ ├── TCR_G.1.bt2 │ ├── TCR_G.2.bt2 │ ├── TCR_G.3.bt2 │ ├── TCR_G.4.bt2 │ ├── TCR_G.fa │ ├── TCR_G.rev.1.bt2 │ └── TCR_G.rev.2.bt2 │ ├── igblast_dbs │ ├── TCR_D.fa │ ├── TCR_D.fa.nhr │ ├── TCR_D.fa.nin │ ├── TCR_D.fa.nog │ ├── TCR_D.fa.nsd │ ├── TCR_D.fa.nsi │ ├── TCR_D.fa.nsq │ ├── TCR_J.fa │ ├── TCR_J.fa.nhr │ ├── TCR_J.fa.nin │ ├── TCR_J.fa.nog │ ├── TCR_J.fa.nsd │ ├── TCR_J.fa.nsi │ ├── TCR_J.fa.nsq │ ├── TCR_V.fa │ ├── TCR_V.fa.nhr │ ├── TCR_V.fa.nin │ ├── TCR_V.fa.nog │ ├── TCR_V.fa.nsd │ ├── TCR_V.fa.nsi │ └── TCR_V.fa.nsq │ ├── invariant_cells.json │ └── raw_seqs │ ├── TCR_A_C.fa │ ├── TCR_A_J.fa │ ├── TCR_A_V.fa │ ├── TCR_B_C.fa │ ├── TCR_B_D.fa │ ├── TCR_B_J.fa │ ├── TCR_B_V.fa │ ├── TCR_D_C.fa │ ├── TCR_D_D.fa │ ├── TCR_D_J.fa │ ├── TCR_D_V.fa │ ├── TCR_G_C.fa │ ├── TCR_G_J.fa │ └── TCR_G_V.fa ├── scripts ├── tracer_assemble.sh └── tracer_summarise.sh ├── setup.py ├── test_data ├── cell1_1.fastq ├── cell1_2.fastq ├── expected_summary │ ├── TCR_summary.txt │ ├── clonotype_network_with_identifiers.dot │ ├── clonotype_network_with_identifiers.pdf │ ├── clonotype_network_without_identifiers.dot │ ├── clonotype_network_without_identifiers.pdf │ ├── clonotype_sizes.pdf │ ├── clonotype_sizes.txt │ ├── recombinants.txt │ ├── reconstructed_lengths_TCRA.pdf │ ├── reconstructed_lengths_TCRA.txt │ ├── reconstructed_lengths_TCRB.pdf │ └── reconstructed_lengths_TCRB.txt └── results │ ├── cell2 │ ├── IgBLAST_output │ │ ├── cell2_TCR_A.IgBLASTOut │ │ └── cell2_TCR_B.IgBLASTOut │ ├── Trinity_output │ │ ├── cell2_TCR_A.Trinity.fasta │ │ ├── cell2_TCR_B.Trinity.fasta │ │ ├── successful_trinity_assemblies.txt │ │ └── unsuccessful_trinity_assemblies.txt │ ├── aligned_reads │ │ ├── cell2_TCR_A.sam │ │ ├── cell2_TCR_A_1.fastq │ │ ├── cell2_TCR_A_2.fastq │ │ ├── cell2_TCR_B.sam │ │ ├── cell2_TCR_B_1.fastq │ │ └── cell2_TCR_B_2.fastq │ ├── expression_quantification │ │ ├── abundance.h5 │ │ ├── abundance.tsv │ │ └── run_info.json │ ├── filtered_TCR_seqs │ │ ├── cell2.pkl │ │ ├── cell2_TCRseqs.fa │ │ └── filtered_TCRs.txt │ └── unfiltered_TCR_seqs │ │ ├── cell2.pkl │ │ ├── cell2_TCRseqs.fa │ │ └── unfiltered_TCRs.txt │ └── cell3 │ ├── IgBLAST_output │ ├── cell3_TCR_A.IgBLASTOut │ └── cell3_TCR_B.IgBLASTOut │ ├── Trinity_output │ ├── cell3_TCR_A.Trinity.fasta │ ├── cell3_TCR_B.Trinity.fasta │ ├── successful_trinity_assemblies.txt │ └── unsuccessful_trinity_assemblies.txt │ ├── aligned_reads │ ├── cell3_TCR_A.sam │ ├── cell3_TCR_A_1.fastq │ ├── cell3_TCR_A_2.fastq │ ├── cell3_TCR_B.sam │ ├── cell3_TCR_B_1.fastq │ └── cell3_TCR_B_2.fastq │ ├── expression_quantification │ ├── abundance.h5 │ ├── abundance.tsv │ └── run_info.json │ ├── filtered_TCR_seqs │ ├── cell3.pkl │ ├── cell3_TCRseqs.fa │ └── filtered_TCRs.txt │ └── unfiltered_TCR_seqs │ ├── cell3.pkl │ ├── cell3_TCRseqs.fa │ └── unfiltered_TCRs.txt ├── tracer ├── tracer.conf └── tracerlib ├── __init__.py ├── __main__.py ├── core.py ├── io.py ├── launcher.py ├── tasks.py ├── tests ├── 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