├── LICENSE ├── README.md ├── Snakefile ├── config.yml ├── database ├── bcelldb.rds ├── germlines │ └── imgt │ │ ├── IMGT.yaml │ │ ├── human │ │ ├── constant │ │ │ ├── imgt_human_IGHC.fasta │ │ │ ├── imgt_human_IGKC.fasta │ │ │ ├── imgt_human_IGLC.fasta │ │ │ ├── imgt_human_TRAC.fasta │ │ │ ├── imgt_human_TRBC.fasta │ │ │ ├── imgt_human_TRDC.fasta │ │ │ └── imgt_human_TRGC.fasta │ │ ├── leader │ │ │ ├── imgt_human_IGHL.fasta │ │ │ ├── imgt_human_IGKL.fasta │ │ │ ├── imgt_human_IGLL.fasta │ │ │ ├── imgt_human_TRAL.fasta │ │ │ ├── imgt_human_TRBL.fasta │ │ │ ├── imgt_human_TRDL.fasta │ │ │ └── imgt_human_TRGL.fasta │ │ └── vdj │ │ │ ├── imgt_human_IGHD.fasta │ │ │ ├── imgt_human_IGHJ.fasta │ │ │ ├── imgt_human_IGHV.fasta │ │ │ ├── imgt_human_IGKJ.fasta │ │ │ ├── imgt_human_IGKV.fasta │ │ │ ├── imgt_human_IGLJ.fasta │ │ │ ├── imgt_human_IGLV.fasta │ │ │ ├── imgt_human_IG_All_J.fasta │ │ │ ├── imgt_human_IG_All_V.fasta │ │ │ ├── imgt_human_TRAJ.fasta │ │ │ ├── imgt_human_TRAV.fasta │ │ │ ├── imgt_human_TRBD.fasta │ │ │ ├── imgt_human_TRBJ.fasta │ │ │ ├── imgt_human_TRBV.fasta │ │ │ ├── imgt_human_TRDD.fasta │ │ │ ├── imgt_human_TRDJ.fasta │ │ │ ├── imgt_human_TRDV.fasta │ │ │ ├── imgt_human_TRGJ.fasta │ │ │ └── imgt_human_TRGV.fasta │ │ ├── mouse │ │ ├── constant │ │ │ ├── imgt_mouse_IGHC.fasta │ │ │ ├── imgt_mouse_IGKC.fasta │ │ │ ├── imgt_mouse_IGLC.fasta │ │ │ ├── imgt_mouse_TRAC.fasta │ │ │ ├── imgt_mouse_TRBC.fasta │ │ │ ├── imgt_mouse_TRDC.fasta │ │ │ └── imgt_mouse_TRGC.fasta │ │ ├── leader │ │ │ ├── imgt_mouse_IGHL.fasta │ │ │ ├── imgt_mouse_IGKL.fasta │ │ │ ├── imgt_mouse_IGLL.fasta │ │ │ ├── imgt_mouse_TRAL.fasta │ │ │ ├── imgt_mouse_TRBL.fasta │ │ │ ├── imgt_mouse_TRDL.fasta │ │ │ └── imgt_mouse_TRGL.fasta │ │ └── vdj │ │ │ ├── imgt_mouse_IGHD.fasta │ │ │ ├── imgt_mouse_IGHJ.fasta │ │ │ ├── imgt_mouse_IGHV.fasta │ │ │ ├── imgt_mouse_IGKJ.fasta │ │ │ ├── imgt_mouse_IGKV.fasta │ │ │ ├── imgt_mouse_IGLJ.fasta │ │ │ ├── imgt_mouse_IGLV.fasta │ │ │ ├── imgt_mouse_IG_All_J.fasta │ │ │ ├── imgt_mouse_IG_All_V.fasta │ │ │ ├── imgt_mouse_TRAJ.fasta │ │ │ ├── imgt_mouse_TRAV.fasta │ │ │ ├── imgt_mouse_TRBD.fasta │ │ │ ├── imgt_mouse_TRBJ.fasta │ │ │ ├── imgt_mouse_TRBV.fasta │ │ │ ├── imgt_mouse_TRDD.fasta │ │ │ ├── imgt_mouse_TRDJ.fasta │ │ │ ├── imgt_mouse_TRDV.fasta │ │ │ ├── imgt_mouse_TRGJ.fasta │ │ │ └── imgt_mouse_TRGV.fasta │ │ └── rhesus │ │ ├── constant │ │ ├── imgt_rhesus_IGHC.fasta │ │ ├── imgt_rhesus_IGKC.fasta │ │ ├── imgt_rhesus_IGLC.fasta │ │ ├── imgt_rhesus_TRAC.fasta │ │ ├── imgt_rhesus_TRBC.fasta │ │ ├── imgt_rhesus_TRDC.fasta │ │ └── imgt_rhesus_TRGC.fasta │ │ ├── leader │ │ ├── imgt_rhesus_IGHL.fasta │ │ ├── imgt_rhesus_IGKL.fasta │ │ ├── imgt_rhesus_IGLL.fasta │ │ ├── imgt_rhesus_TRAL.fasta │ │ ├── imgt_rhesus_TRBL.fasta │ │ ├── imgt_rhesus_TRDL.fasta │ │ └── imgt_rhesus_TRGL.fasta │ │ └── vdj │ │ ├── imgt_rhesus_IGHD.fasta │ │ ├── imgt_rhesus_IGHJ.fasta │ │ ├── imgt_rhesus_IGHV.fasta │ │ ├── imgt_rhesus_IGKJ.fasta │ │ ├── imgt_rhesus_IGKV.fasta │ │ ├── imgt_rhesus_IGLJ.fasta │ │ ├── imgt_rhesus_IGLV.fasta │ │ ├── imgt_rhesus_IG_All_J.fasta │ │ ├── imgt_rhesus_IG_All_V.fasta │ │ ├── imgt_rhesus_TRAJ.fasta │ │ ├── imgt_rhesus_TRAV.fasta │ │ ├── imgt_rhesus_TRBD.fasta │ │ ├── imgt_rhesus_TRBJ.fasta │ │ ├── imgt_rhesus_TRBV.fasta │ │ ├── imgt_rhesus_TRDD.fasta │ │ ├── imgt_rhesus_TRDJ.fasta │ │ ├── imgt_rhesus_TRDV.fasta │ │ ├── imgt_rhesus_TRGJ.fasta │ │ └── imgt_rhesus_TRGV.fasta └── igblast │ ├── database │ ├── imgt_human_ig_d.nhr │ ├── imgt_human_ig_d.nin │ ├── imgt_human_ig_d.nog │ ├── imgt_human_ig_d.nsd │ ├── imgt_human_ig_d.nsi │ ├── imgt_human_ig_d.nsq │ ├── imgt_human_ig_j.nhr │ ├── imgt_human_ig_j.nin │ ├── imgt_human_ig_j.nog │ ├── imgt_human_ig_j.nsd │ ├── imgt_human_ig_j.nsi │ ├── imgt_human_ig_j.nsq │ ├── imgt_human_ig_v.nhr │ ├── imgt_human_ig_v.nin │ ├── imgt_human_ig_v.nog │ ├── imgt_human_ig_v.nsd │ ├── imgt_human_ig_v.nsi │ ├── imgt_human_ig_v.nsq │ ├── imgt_human_tr_d.nhr │ ├── imgt_human_tr_d.nin │ ├── imgt_human_tr_d.nog │ ├── imgt_human_tr_d.nsd │ ├── imgt_human_tr_d.nsi │ ├── imgt_human_tr_d.nsq │ ├── imgt_human_tr_j.nhr │ ├── imgt_human_tr_j.nin │ ├── imgt_human_tr_j.nog │ ├── imgt_human_tr_j.nsd │ ├── imgt_human_tr_j.nsi │ ├── imgt_human_tr_j.nsq │ ├── imgt_human_tr_v.nhr │ ├── imgt_human_tr_v.nin │ ├── imgt_human_tr_v.nog │ ├── imgt_human_tr_v.nsd │ ├── imgt_human_tr_v.nsi │ ├── imgt_human_tr_v.nsq │ ├── imgt_mouse_ig_d.nhr │ ├── imgt_mouse_ig_d.nin │ ├── imgt_mouse_ig_d.nog │ ├── imgt_mouse_ig_d.nsd │ ├── imgt_mouse_ig_d.nsi │ ├── imgt_mouse_ig_d.nsq │ ├── imgt_mouse_ig_j.nhr │ ├── imgt_mouse_ig_j.nin │ ├── imgt_mouse_ig_j.nog │ ├── imgt_mouse_ig_j.nsd │ ├── imgt_mouse_ig_j.nsi │ ├── imgt_mouse_ig_j.nsq │ ├── imgt_mouse_ig_v.nhr │ ├── imgt_mouse_ig_v.nin │ ├── imgt_mouse_ig_v.nog │ ├── imgt_mouse_ig_v.nsd │ ├── imgt_mouse_ig_v.nsi │ ├── imgt_mouse_ig_v.nsq │ ├── imgt_mouse_tr_d.nhr │ ├── imgt_mouse_tr_d.nin │ ├── imgt_mouse_tr_d.nog │ ├── imgt_mouse_tr_d.nsd │ ├── imgt_mouse_tr_d.nsi │ ├── imgt_mouse_tr_d.nsq │ ├── imgt_mouse_tr_j.nhr │ ├── imgt_mouse_tr_j.nin │ ├── imgt_mouse_tr_j.nog │ ├── imgt_mouse_tr_j.nsd │ ├── imgt_mouse_tr_j.nsi │ ├── imgt_mouse_tr_j.nsq │ ├── imgt_mouse_tr_v.nhr │ ├── imgt_mouse_tr_v.nin │ ├── imgt_mouse_tr_v.nog │ ├── imgt_mouse_tr_v.nsd │ ├── imgt_mouse_tr_v.nsi │ ├── imgt_mouse_tr_v.nsq │ ├── imgt_rhesus_ig_d.nhr │ ├── imgt_rhesus_ig_d.nin │ ├── imgt_rhesus_ig_d.nog │ ├── imgt_rhesus_ig_d.nsd │ ├── imgt_rhesus_ig_d.nsi │ ├── imgt_rhesus_ig_d.nsq │ ├── imgt_rhesus_ig_j.nhr │ ├── imgt_rhesus_ig_j.nin │ ├── imgt_rhesus_ig_j.nog │ ├── imgt_rhesus_ig_j.nsd │ ├── imgt_rhesus_ig_j.nsi │ ├── imgt_rhesus_ig_j.nsq │ ├── imgt_rhesus_ig_v.nhr │ ├── imgt_rhesus_ig_v.nin │ ├── imgt_rhesus_ig_v.nog │ ├── imgt_rhesus_ig_v.nsd │ ├── imgt_rhesus_ig_v.nsi │ ├── imgt_rhesus_ig_v.nsq │ ├── imgt_rhesus_tr_d.nhr │ ├── imgt_rhesus_tr_d.nin │ ├── imgt_rhesus_tr_d.nog │ ├── imgt_rhesus_tr_d.nsd │ ├── imgt_rhesus_tr_d.nsi │ ├── imgt_rhesus_tr_d.nsq │ ├── imgt_rhesus_tr_j.nhr │ ├── imgt_rhesus_tr_j.nin │ ├── imgt_rhesus_tr_j.nog │ ├── imgt_rhesus_tr_j.nsd │ ├── imgt_rhesus_tr_j.nsi │ ├── imgt_rhesus_tr_j.nsq │ ├── imgt_rhesus_tr_v.nhr │ ├── imgt_rhesus_tr_v.nin │ ├── imgt_rhesus_tr_v.nog │ ├── imgt_rhesus_tr_v.nsd │ ├── imgt_rhesus_tr_v.nsi │ ├── imgt_rhesus_tr_v.nsq │ ├── mouse_gl_VDJ.tar │ └── rhesus_monkey_VJ.tar │ ├── fasta │ ├── imgt_human_ig_d.fasta │ ├── imgt_human_ig_j.fasta │ ├── imgt_human_ig_v.fasta │ ├── imgt_human_tr_d.fasta │ ├── imgt_human_tr_j.fasta │ ├── imgt_human_tr_v.fasta │ ├── imgt_mouse_ig_d.fasta │ ├── imgt_mouse_ig_j.fasta │ ├── imgt_mouse_ig_v.fasta │ ├── imgt_mouse_tr_d.fasta │ ├── imgt_mouse_tr_j.fasta │ ├── imgt_mouse_tr_v.fasta │ ├── imgt_rhesus_ig_d.fasta │ ├── imgt_rhesus_ig_j.fasta │ ├── imgt_rhesus_ig_v.fasta │ ├── imgt_rhesus_tr_d.fasta │ ├── imgt_rhesus_tr_j.fasta │ └── imgt_rhesus_tr_v.fasta │ ├── internal_data │ ├── human │ │ ├── human.ndm.imgt │ │ ├── human.ndm.kabat │ │ ├── human.pdm.imgt │ │ ├── human.pdm.kabat │ │ ├── human_TR_V.nhr │ │ ├── human_TR_V.nin │ │ ├── human_TR_V.nog │ │ ├── human_TR_V.nsd │ │ ├── human_TR_V.nsi │ │ ├── human_TR_V.nsq │ │ ├── human_TR_V.phr │ │ ├── human_TR_V.pin │ │ ├── human_TR_V.pog │ │ ├── human_TR_V.psd │ │ ├── human_TR_V.psi │ │ ├── human_TR_V.psq │ │ ├── human_V.nhr │ │ ├── human_V.nin │ │ ├── human_V.nog │ │ ├── human_V.nsd │ │ ├── human_V.nsi │ │ ├── human_V.nsq │ │ ├── human_V.phr │ │ ├── human_V.pin │ │ ├── human_V.pog │ │ ├── human_V.psd │ │ ├── human_V.psi │ │ └── human_V.psq │ ├── mouse │ │ ├── mouse.ndm.imgt │ │ ├── mouse.ndm.kabat │ │ ├── mouse.pdm.imgt │ │ ├── mouse.pdm.kabat │ │ ├── mouse_TR_V.nhr │ │ ├── mouse_TR_V.nin │ │ ├── mouse_TR_V.nog │ │ ├── mouse_TR_V.nsd │ │ ├── mouse_TR_V.nsi │ │ ├── mouse_TR_V.nsq │ │ ├── mouse_TR_V.phr │ │ ├── mouse_TR_V.pin │ │ ├── mouse_TR_V.pog │ │ ├── mouse_TR_V.psd │ │ ├── mouse_TR_V.psi │ │ ├── mouse_TR_V.psq │ │ ├── mouse_V.nhr │ │ ├── mouse_V.nin │ │ ├── mouse_V.nog │ │ ├── mouse_V.nsd │ │ ├── mouse_V.nsi │ │ ├── mouse_V.nsq │ │ ├── mouse_V.phr │ │ ├── mouse_V.pin │ │ ├── mouse_V.pog │ │ ├── mouse_V.psd │ │ ├── mouse_V.psi │ │ └── mouse_V.psq │ ├── rabbit │ │ ├── rabbit.ndm.imgt │ │ ├── rabbit.ndm.kabat │ │ ├── rabbit.pdm.imgt │ │ ├── rabbit.pdm.kabat │ │ ├── rabbit_V.nhr │ │ ├── rabbit_V.nin │ │ ├── rabbit_V.nog │ │ ├── rabbit_V.nsd │ │ ├── rabbit_V.nsi │ │ ├── rabbit_V.nsq │ │ ├── rabbit_V.phr │ │ ├── rabbit_V.pin │ │ ├── rabbit_V.pog │ │ ├── rabbit_V.psd │ │ ├── rabbit_V.psi │ │ └── rabbit_V.psq │ ├── rat │ │ ├── rat.ndm.imgt │ │ ├── rat.ndm.kabat │ │ ├── rat.pdm.imgt │ │ ├── rat.pdm.kabat │ │ ├── rat_V.nhr │ │ ├── rat_V.nin │ │ ├── rat_V.nog │ │ ├── rat_V.nsd │ │ ├── rat_V.nsi │ │ ├── rat_V.nsq │ │ ├── rat_V.phr │ │ ├── rat_V.pin │ │ ├── rat_V.pog │ │ ├── rat_V.psd │ │ ├── rat_V.psi │ │ └── rat_V.psq │ └── rhesus_monkey │ │ ├── CVS │ │ ├── Entries │ │ ├── Repository │ │ └── Root │ │ ├── rhesus_monkey.ndm.imgt │ │ ├── rhesus_monkey.ndm.kabat │ │ ├── rhesus_monkey.pdm.imgt │ │ ├── rhesus_monkey.pdm.kabat │ │ ├── rhesus_monkey_D.nhr │ │ ├── rhesus_monkey_D.nin │ │ ├── rhesus_monkey_D.nog │ │ ├── rhesus_monkey_D.nsd │ │ ├── rhesus_monkey_D.nsi │ │ ├── rhesus_monkey_D.nsq │ │ ├── rhesus_monkey_J.nhr │ │ ├── rhesus_monkey_J.nin │ │ ├── rhesus_monkey_J.nog │ │ ├── rhesus_monkey_J.nsd │ │ ├── rhesus_monkey_J.nsi │ │ ├── rhesus_monkey_J.nsq │ │ ├── rhesus_monkey_V.nhr │ │ ├── rhesus_monkey_V.nin │ │ ├── rhesus_monkey_V.nog │ │ ├── rhesus_monkey_V.nsd │ │ ├── rhesus_monkey_V.nsi │ │ ├── rhesus_monkey_V.nsq │ │ ├── rhesus_monkey_V.phr │ │ ├── rhesus_monkey_V.pin │ │ ├── rhesus_monkey_V.pog │ │ ├── rhesus_monkey_V.psd │ │ ├── rhesus_monkey_V.psi │ │ └── rhesus_monkey_V.psq │ └── optional_file │ ├── human_gl.aux │ ├── human_gl.aux.testonly │ ├── mouse_gl.aux │ ├── rabbit_gl.aux │ ├── rat_gl.aux │ └── rhesus_monkey_gl.aux ├── img ├── img1.png ├── img10.png ├── img2.png ├── img3.png ├── img4.png ├── img5.png ├── img6.png ├── img7.png ├── img8.png └── img9.png └── scripts ├── IgPairs.pl ├── ParseToCircos2.R ├── SHM_analysis.R ├── batch_ab1tofastq.py ├── correct_regions.py ├── data_integration.py ├── generate_xlsx.py ├── hydrophobicity_analysis.R ├── monkey_ig_tookit.pl └── prepare_data.sh /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/stratust/igpipeline/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/stratust/igpipeline/HEAD/README.md -------------------------------------------------------------------------------- /Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/stratust/igpipeline/HEAD/Snakefile 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