├── .gitattributes ├── .gitignore ├── LICENSE ├── README.md ├── Snakefile ├── config.yml ├── config ├── alt_motifs.txt ├── file_layout.yaml └── refgenome.csv ├── datasets.csv ├── environment.yml ├── incomming ├── model └── teloseq_bonito.0.6.2_R941C.fine_turned.tar.gz ├── report_template └── 20221130_telomere_report_template.py.ipynb ├── rules ├── common.smk ├── envs │ ├── bedtools.yml │ ├── blastn.yml │ ├── clair3.yml │ ├── fastcat.yml │ ├── freebayes.yml │ ├── hapcut2.yml │ ├── jupyter.yml │ ├── kmc.yml │ ├── lra.yml │ ├── medaka.yml │ ├── minimap2.yml │ ├── mosdepth.yml │ ├── nanocallers.yml │ ├── nanofilt.yml │ ├── ncrf.yml │ ├── nextflow.yml │ ├── samtools.yml │ ├── seqkit.yml │ ├── sniffles.yml │ ├── vg.yml │ └── yacrd.yml ├── filterbam.smk ├── haplotyping.smk ├── ingest.smk ├── mapping.smk ├── modbases.smk ├── repeat_finder.smk ├── reports.smk ├── stats.smk ├── telomere_variants.smk ├── tvr.smk └── variants.smk ├── scripts ├── Restriction_digest_reads.py ├── TVR_signal.py ├── bam_stats.py ├── build_chrom_ends_bedfile.py ├── build_telomere_reference.py ├── count_kmers.py ├── filter_bam_2023.py ├── ncrf.summary.stats.py ├── ncrf2bed.py ├── ncrf_cat.py ├── ncrf_summary.py ├── plot_methlyation_from_modkit.py ├── split_telomere_by_arms.py └── telomeric_variant_repeats.py └── wrappers ├── bam_stats ├── environment.yaml └── wrapper.py └── downloader ├── environment.yaml └── wrapper.py /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Priyesh000/teloseq/HEAD/.gitattributes -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Priyesh000/teloseq/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 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