├── .github └── workflows │ └── stale.yml ├── .gitignore ├── LICENSE ├── README.md ├── azure-pipelines.yml ├── bin ├── .pylintrc ├── ntjoin.py ├── ntjoin_assemble.py ├── ntjoin_overlap.py ├── ntjoin_run.py ├── ntjoin_utils.py ├── overlap_region.py ├── path_node.py └── read_fasta.py ├── logo.png ├── ntJoin ├── ntjoin-logo.png ├── requirements.txt ├── setup.py └── tests ├── expected_outputs ├── f-f_test.mx.dot ├── f-f_test.path ├── f-f_test.scaf.f-f.fa.k32.w1000.tsv.unassigned.bed ├── ref.fa.fai ├── ref.fa.k32.w1000.tsv ├── scaf.f-f.fa.fai ├── scaf.f-f.fa.k32.w1000.n1.all.scaffolds.fa ├── scaf.f-f.fa.k32.w1000.n1.assigned.scaffolds.fa ├── scaf.f-f.fa.k32.w1000.n1.unassigned.scaffolds.fa └── scaf.f-f.fa.k32.w1000.tsv ├── ntjoin_test.py ├── ref.fa ├── ref.longer.fa ├── ref.multiple.fa ├── scaf.f-f.copy.fa ├── scaf.f-f.fa ├── scaf.f-f.overlapping.fa ├── scaf.f-f.termN.fa ├── scaf.f-f.termN.unassigned.fa ├── scaf.f-r.fa ├── scaf.f-r.overlapping.fa ├── scaf.misassembled.f-f.r-r.fa ├── 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