├── .gitignore ├── Dockerfile ├── LICENSE ├── Makefile ├── README.md ├── guppy5_stats ├── dels_cm.npy ├── inss_cm.npy ├── nps_cm.npy └── subs_cm.npy ├── img └── npore_pileup.png ├── requirements.txt ├── scripts ├── align.sh ├── calc_beds.sh ├── happy.sh ├── plot_legend.py ├── plot_results.py ├── plot_sankey.py ├── purity.sh ├── realign_pipeline.sh ├── sankey.py └── tag_unphased.py ├── setup.py ├── src ├── aln.pyx ├── bam.pyx ├── bed.py ├── cfg.py ├── cig.pyx ├── filter.py ├── purity.py ├── realign.py ├── standardize_vcf.py ├── util.py └── vcf.py └── test ├── align.py ├── data ├── npore_realigned.sam ├── reads.bam ├── reads.bam.bai ├── reads.fastq ├── reads.sam ├── ref.fasta └── ref.fasta.fai ├── generate_bam.py ├── get_np_info.py ├── profile_alignment.ipynb ├── realign.sh ├── test_std_ref.fasta ├── test_std_vcf.sh └── test_std_vcf.vcf /.gitignore: -------------------------------------------------------------------------------- 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