├── .DS_Store ├── ._README.md ├── ._TC_hunter.nf ├── ._TC_hunter_BWA.nf ├── .nextflow ├── cache │ ├── 038ba64a-8870-41a5-a463-dcc6dd3a0eb6 │ │ ├── db │ │ │ ├── 000003.log │ │ │ ├── CURRENT │ │ │ ├── LOCK │ │ │ └── MANIFEST-000002 │ │ └── index.irreverent_fermat │ ├── 0a3c0dee-7164-4d6c-8907-a3f38e133cdb │ │ ├── db │ │ │ ├── 000003.log │ │ │ ├── CURRENT │ │ │ ├── LOCK │ │ │ └── MANIFEST-000002 │ │ └── index.maniac_knuth │ ├── 124884f5-089f-4596-ac14-38ab849e88b1 │ │ ├── db │ │ │ ├── 000003.log │ │ │ ├── CURRENT │ │ │ ├── LOCK │ │ │ └── MANIFEST-000002 │ │ └── index.distraught_miescher │ ├── 2532544a-8b21-4e7a-aecd-24d7741274f3 │ │ ├── db │ │ │ ├── 000003.log │ │ │ ├── CURRENT │ │ │ ├── LOCK │ │ │ └── MANIFEST-000002 │ │ └── index.suspicious_lamport │ ├── 2c219ea4-9338-48cf-a5fe-ab815a173537 │ │ ├── db │ │ │ ├── 000003.log │ │ │ ├── CURRENT │ │ │ ├── LOCK │ │ │ └── MANIFEST-000002 │ │ └── index.soggy_noyce │ ├── 373a5415-737a-49c1-9352-c38fd85feaa4 │ │ ├── db │ │ │ ├── 000003.log │ │ │ ├── CURRENT │ │ │ ├── LOCK │ │ │ └── MANIFEST-000002 │ │ └── index.nice_almeida │ ├── 52a9abb1-edba-41de-9eee-bb1b75ce6bb2 │ │ ├── db │ │ │ ├── 000003.log │ │ │ ├── CURRENT │ │ │ ├── LOCK │ │ │ └── MANIFEST-000002 │ │ └── index.fabulous_gautier │ ├── 55074a91-6b92-4757-aab6-1ba086378f2d │ │ ├── db │ │ │ ├── 000003.log │ │ │ ├── CURRENT │ │ │ ├── LOCK │ │ │ └── MANIFEST-000002 │ │ └── index.hopeful_stonebraker │ ├── 56add4a8-4203-4692-ab7e-3d25dc7a9930 │ │ ├── db │ │ │ ├── 000003.log │ │ │ ├── CURRENT │ │ │ ├── LOCK │ │ │ └── MANIFEST-000002 │ │ └── index.suspicious_pike │ ├── 69584c19-de88-4e32-9e3f-9cf60a89a618 │ │ ├── db │ │ │ ├── 000003.log │ │ │ ├── CURRENT │ │ │ ├── LOCK │ │ │ └── MANIFEST-000002 │ │ └── index.marvelous_miescher │ ├── 6a940234-aa9d-47c4-8e39-5cb1c4e1476b │ │ ├── db │ │ │ ├── 000003.log │ │ │ ├── CURRENT │ │ │ ├── LOCK │ │ │ └── MANIFEST-000002 │ │ └── index.compassionate_avogadro │ ├── 8ba965f3-c443-4277-b973-b57367ba23fd │ │ ├── db │ │ │ ├── 000003.log │ │ │ ├── CURRENT │ │ │ ├── LOCK │ │ │ └── MANIFEST-000002 │ │ └── index.astonishing_mendel │ ├── a565bcca-b7ea-4744-b861-cbc1c3d8c2eb │ │ ├── db │ │ │ ├── 000003.log │ │ │ ├── CURRENT │ │ │ ├── LOCK │ │ │ └── MANIFEST-000002 │ │ └── index.hopeful_wiles │ ├── b8a3c529-11dd-4d04-b0d7-a693cb42bb2a │ │ ├── db │ │ │ ├── 000003.log │ │ │ ├── CURRENT │ │ │ ├── LOCK │ │ │ └── MANIFEST-000002 │ │ └── index.compassionate_babbage │ ├── bdb94b3d-0f77-43c3-ad14-940612f760e0 │ │ ├── db │ │ │ ├── 000003.log │ │ │ ├── CURRENT │ │ │ ├── LOCK │ │ │ └── MANIFEST-000002 │ │ └── index.jovial_brahmagupta │ ├── c96ccd1e-a70d-4827-ba92-15a2cc89cc42 │ │ ├── db │ │ │ ├── 000003.log │ │ │ ├── CURRENT │ │ │ ├── LOCK │ │ │ └── MANIFEST-000002 │ │ └── index.chaotic_ampere │ ├── cd5704e4-bab5-4d0a-9b9c-fd4aca0480dc │ │ ├── db │ │ │ ├── 000003.log │ │ │ ├── CURRENT │ │ │ ├── LOCK │ │ │ └── MANIFEST-000002 │ │ └── index.irreverent_ardinghelli │ ├── d62a6c39-c860-4476-891d-54813e453a59 │ │ ├── db │ │ │ ├── 000003.log │ │ │ ├── CURRENT │ │ │ ├── LOCK │ │ │ └── MANIFEST-000002 │ │ └── index.curious_stonebraker │ ├── dd45f4d0-85ee-43d1-941d-7ec0bc105392 │ │ ├── db │ │ │ ├── 000003.log │ │ │ ├── CURRENT │ │ │ ├── LOCK │ │ │ └── MANIFEST-000002 │ │ └── index.evil_shirley │ └── fcf3ea01-9708-43b8-b1f3-3ed6a4a3e1fd │ │ ├── db │ │ ├── 000003.log │ │ ├── CURRENT │ │ ├── LOCK │ │ └── MANIFEST-000002 │ │ └── index.golden_shirley └── history ├── LICENSE ├── Plots ├── ._TC_hunter_pipeline.png ├── ._circlize.png ├── ._softclipped.png ├── ._tc_hunter_out.png ├── TC_hunter_pipeline.png ├── circlize.png ├── softclipped.png └── tc_hunter_out.png ├── README.md ├── README.md~ ├── Scripts ├── ExtractConstruct.py ├── ExtractConstruct.sh ├── FindLinks.py ├── Nextflow_env.txt ├── TC_hunter.yml ├── biomart.R ├── circlize.R ├── createHistogram.py ├── createKaryotype.py ├── createOutput.py └── runSoftClipExtraction.sh ├── TC_hunter.nf ├── TC_hunter_BWA.nf ├── Test_data ├── ._testrun.config ├── JointRefGenome.fasta ├── 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