├── README.md ├── accessibility_masks ├── README.md ├── acc_mask.yml ├── code │ ├── baseq_mask.py │ ├── baseq_mask_wrapper.sh │ ├── coverage_mask.py │ ├── coverage_mask_wrapper.sh │ ├── get_median_coverage.sh │ ├── mapq_mask.py │ ├── mapq_mask_prep.sh │ └── mapq_mask_wrapper.sh └── data │ ├── references │ ├── autosomes.bed │ └── chm13v2.0.PAR.bed │ └── sample.info ├── alignments └── lastz │ └── EDFig3a_dotplot_idy.R ├── amplicons_and_palindromes ├── amplicons │ ├── 1_extract_amplicons.sh │ ├── 2_map_extracted_amplicons_to_T2T_Y.sh │ ├── README.md │ ├── align_extracted_amplicons.sh │ └── hg38.amplicons.colors.bed ├── intrachromosomal_similarity │ ├── README.md │ ├── chrY.2.7.hardmasked.windows.sorted.bam.f1-6.txt │ ├── hardmasked.identities.txt │ ├── parse_bam.py │ ├── plot_intrachromosomal_identity.Rnw │ ├── split_Y_chromosome_into_windows_and_calculate_intrachromosomal_similarity.sh │ └── window_identity.txt └── palindromes │ ├── 1_extract_palindrome_arms_from_dotplot.sh │ ├── 2_align_palindrome_arms_that_include_flanks.sh │ ├── 3_extract_palindrome_arms_after_stitcher_adjustment.sh │ ├── 4_align_adjusted_palindrome_arms.sh │ ├── P4-P5.hg002_v2.7.fixed.bed │ ├── P4-P5.hg002_v2.7.initial.bed │ ├── P4.hg002.selfalign │ ├── P5.hg002.selfalign │ ├── P6.hg002.selfalign │ ├── P7.hg002.selfalign │ ├── P8.hg002.selfalign │ ├── README.md │ └── chrY.2.7.genome.txt ├── epigenetics ├── .gitignore ├── 221019_nanopolish_nanonome_setup.pdf ├── README.md ├── hg002_chrY_methylation_resources.csv ├── nanopolish_methylation_scripts │ ├── README.md │ ├── align_hg002.sh │ ├── cpg_nanonome_CHM13v2.0_nanopolish_processing.sh │ ├── cpg_nanonome_CHM13v2.7_nanopolish_processing.sh │ ├── cpggpc_nanonome_CHM13v2.0_nanopolish_call_meth.sh │ ├── cpggpc_nanonome_CHM13v2.7_nanopolish_call_meth.sh │ ├── filter_hg002.sh │ ├── merge_hg002.sh │ └── nanonome_cpggpc_call_meth.sh ├── r_analysis │ ├── 220712_methylation_analysis.Rmd │ ├── README.md │ ├── bw.Rmd │ └── raw_figures │ │ ├── 220912_guppy_wgbs.pdf │ │ ├── 220912_hg002_corrplot.pdf │ │ ├── 220912_nanopolish_wgbs.pdf │ │ └── 220912_primrose_wgbs.pdf ├── remora_methylation_processing │ ├── README.md │ ├── config │ │ └── config.yaml │ ├── reports │ │ └── alignment │ │ │ ├── chm13v2.0_bam_runid_0003faf087e574e8a68bf1175367b4d975d5f9ea_5_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_0003faf087e574e8a68bf1175367b4d975d5f9ea_6_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_0003faf087e574e8a68bf1175367b4d975d5f9ea_9_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_467aee0874eee5c3232a5976425cca439093d0ba_0_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_467aee0874eee5c3232a5976425cca439093d0ba_1_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_467aee0874eee5c3232a5976425cca439093d0ba_4_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_5fb311a13122eeb62f8b8bd9a9e225cc2894453e_10_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_5fb311a13122eeb62f8b8bd9a9e225cc2894453e_7_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_5fb311a13122eeb62f8b8bd9a9e225cc2894453e_9_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_7d89fd496ba22768020724f387ace3fc20ec4c49_2_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_7d89fd496ba22768020724f387ace3fc20ec4c49_3_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_7d89fd496ba22768020724f387ace3fc20ec4c49_4_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_7d89fd496ba22768020724f387ace3fc20ec4c49_5_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_7d89fd496ba22768020724f387ace3fc20ec4c49_7_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_7d89fd496ba22768020724f387ace3fc20ec4c49_8_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_7d89fd496ba22768020724f387ace3fc20ec4c49_9_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_de0624057e96dccac9337e021ebc8f8f94c5141d_0_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_de0624057e96dccac9337e021ebc8f8f94c5141d_3_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_de0624057e96dccac9337e021ebc8f8f94c5141d_5_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_e558f8d77002e7ee60a4b938e2f2a418d2499203_1_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_e558f8d77002e7ee60a4b938e2f2a418d2499203_2_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_e558f8d77002e7ee60a4b938e2f2a418d2499203_4_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_e558f8d77002e7ee60a4b938e2f2a418d2499203_5_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_f0ac6a7510babcf1880222e874ab44a8dcea29da_2_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_f0ac6a7510babcf1880222e874ab44a8dcea29da_3_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_f0ac6a7510babcf1880222e874ab44a8dcea29da_4_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_f0ac6a7510babcf1880222e874ab44a8dcea29da_5_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_faac3ceebe010005f96f1f5de033e0e5606ddf3f_0_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_faac3ceebe010005f96f1f5de033e0e5606ddf3f_10_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_faac3ceebe010005f96f1f5de033e0e5606ddf3f_1_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_faac3ceebe010005f96f1f5de033e0e5606ddf3f_4_0.bam.log │ │ │ ├── chm13v2.0_bam_runid_faac3ceebe010005f96f1f5de033e0e5606ddf3f_5_0.bam.log │ │ │ └── chm13v2.0_bam_runid_faac3ceebe010005f96f1f5de033e0e5606ddf3f_8_0.bam.log │ └── workflow │ │ ├── Snakefile │ │ ├── envs │ │ ├── meth_alignment.yaml │ │ └── modbam2bed.yaml │ │ ├── history.txt │ │ └── rules │ │ ├── align_process_remora_bams.smk │ │ └── modbam2bed.smk └── wgbs_pacbio_processing │ ├── README.md │ ├── config │ └── config.yaml │ ├── reports │ ├── bismark │ │ ├── bismark2bedgraph_seqc2_emseq_lab1_CpG.log │ │ ├── bismark2bedgraph_seqc2_emseq_lab2_CpG.log │ │ ├── bismark2bedgraph_seqc2_methylseq_CpG.log │ │ ├── coverage2cytosine_methylseq_CpG.log │ │ ├── coverage2cytosine_seqc2_emseq_lab1_CpG.log │ │ ├── coverage2cytosine_seqc2_emseq_lab2_CpG.log │ │ ├── dedup.emseq_SRR13051139_pe.log │ │ ├── dedup.emseq_SRR13051140_pe.log │ │ ├── dedup.emseq_SRR13051141_pe.log │ │ ├── dedup.emseq_SRR13051142_pe.log │ │ ├── dedup.methylseq_SRR13051101_pe.log │ │ ├── dedup.methylseq_SRR13051102_pe.log │ │ ├── dedup.methylseq_SRR13051103_pe.log │ │ ├── dedup.methylseq_SRR13051104_pe.log │ │ ├── dedup.methylseq_SRR13051105_pe.log │ │ ├── dedup.methylseq_SRR13051106_pe.log │ │ ├── emseq_SRR13051139.log │ │ ├── emseq_SRR13051140.log │ │ ├── emseq_SRR13051141.log │ │ ├── emseq_SRR13051142.log │ │ ├── extraction_emseq_SRR13051139_pe.deduplicated.log │ │ ├── extraction_emseq_SRR13051140_pe.deduplicated.log │ │ ├── extraction_emseq_SRR13051141_pe.deduplicated.log │ │ ├── extraction_emseq_SRR13051142_pe.deduplicated.log │ │ ├── extraction_methylseq_SRR13051101.deduplicated.log │ │ ├── extraction_methylseq_SRR13051102.deduplicated.log │ │ ├── extraction_methylseq_SRR13051103.deduplicated.log │ │ ├── extraction_methylseq_SRR13051104.deduplicated.log │ │ ├── extraction_methylseq_SRR13051105.deduplicated.log │ │ ├── extraction_methylseq_SRR13051106.deduplicated.log │ │ ├── mbias_emseq_SRR13051139_pe.deduplicated.log │ │ ├── mbias_emseq_SRR13051140_pe.deduplicated.log │ │ ├── mbias_emseq_SRR13051141_pe.deduplicated.log │ │ ├── mbias_emseq_SRR13051142_pe.deduplicated.log │ │ ├── mbias_methylseq_SRR13051101.deduplicated.log │ │ ├── mbias_methylseq_SRR13051102.deduplicated.log │ │ ├── mbias_methylseq_SRR13051103.deduplicated.log │ │ ├── mbias_methylseq_SRR13051104.deduplicated.log │ │ ├── mbias_methylseq_SRR13051105.deduplicated.log │ │ ├── mbias_methylseq_SRR13051106.deduplicated.log │ │ ├── methylseq_SRR13051101.log │ │ ├── methylseq_SRR13051102.log │ │ ├── methylseq_SRR13051103.log │ │ ├── methylseq_SRR13051104.log │ │ ├── methylseq_SRR13051105.log │ │ └── methylseq_SRR13051106.log │ ├── bowtie2.bsgenomeprep.log │ └── trim │ │ ├── emseq_sr_SRR13051139_trim.log │ │ ├── emseq_sr_SRR13051140_trim.log │ │ ├── emseq_sr_SRR13051141_trim.log │ │ ├── emseq_sr_SRR13051142_trim.log │ │ ├── methylseq_sr_SRR13051101_trim.log │ │ ├── methylseq_sr_SRR13051102_trim.log │ │ ├── methylseq_sr_SRR13051103_trim.log │ │ ├── methylseq_sr_SRR13051104_trim.log │ │ ├── methylseq_sr_SRR13051105_trim.log │ │ └── methylseq_sr_SRR13051106_trim.log │ └── workflow │ ├── Snakefile │ ├── envs │ ├── aligners.yaml │ ├── cutadapt.yaml │ ├── fastp.yaml │ ├── ffq.yaml │ ├── modbam2bed.yaml │ ├── mosdepth.yaml │ ├── phasing.yaml │ └── samtools.yaml │ ├── rules │ ├── bismark_download.smk │ ├── bismark_genome_prep.smk │ ├── concatenate_index_genomes.smk │ ├── download_control_genomes.smk │ ├── download_data.smk │ ├── download_human_genome.smk │ ├── emseq_bismark2bedgraph.smk │ ├── emseq_bismark_align.smk │ ├── emseq_bismark_deduplicate.smk │ ├── emseq_coverage2cytosine.smk │ ├── emseq_extraction.smk │ ├── emseq_mbias.smk │ ├── merge_technolgies.smk │ ├── methylseq_bismark2bedgraph.smk │ ├── methylseq_bismark_align.smk │ ├── methylseq_bismark_deduplicate.smk │ ├── methylseq_coverage2cytosine.smk │ ├── methylseq_extraction.smk │ ├── methylseq_mbias.smk │ ├── modbam2bed.smk │ └── short_read_trim.smk │ └── scripts │ ├── 220504_mbias_plots.Rmd │ ├── 220706_mbias_plots.Rmd │ └── 220712_methylation_analysis.Rmd ├── igv_sessions ├── Fig1_Overview.xml ├── Fig2_AmpliconicGenes_In_CompositeRepeats.xml ├── Fig3_Centromere.xml ├── Fig5b_HSat_Idy.xml ├── Fig6g_v1_GRCh38Y_DYZ19.xml ├── Fig6g_v2_HG002Y_DYZ19.xml └── README.md ├── liftover └── gencodeV35 │ ├── README │ ├── chm13v2_to_grch38.v1_nflo.commands │ ├── chm13v2_to_grch38.wfmash.commands │ ├── filter_duplicate_intervals.pl │ ├── grch38_to_chm13v2.v1_nflo.commands │ ├── grch38_to_chm13v2.wfmash.commands │ ├── sh.lift_from_chm13v2_to_grch38 │ └── sh.lift_from_grch38_to_chm13v2 ├── refseq-contamination ├── README.txt ├── combine.pl ├── coverage.pl ├── extract-names.pl ├── plot │ ├── input │ │ ├── chm13v2-hits-per-query.filt.hsat.category │ │ ├── chm13v2-hits-per-query.filt.hsat.category.chm13v2_only │ │ ├── chm13v2-queries-per-10k-window │ │ ├── chm13v2only-queries-per-10k-window │ │ ├── grch38-hits-per-query.filt.hsat.category │ │ └── grch38-queries-per-10k-window │ ├── output │ │ ├── refseq_contam.pdf │ │ ├── refseq_contam.png │ │ ├── refseq_contam_len.pdf │ │ └── refseq_contam_len.png │ └── src │ │ └── Contamination.R ├── run-kmers-chm13.sh └── 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