├── .gitignore ├── Abstract └── abstract.tex ├── Acknowledgement └── acknowledgement.tex ├── Appendix1 └── appendix1.tex ├── Appendix2 └── appendix2.tex ├── ChangeLog.md ├── Chapter1 ├── Figs │ ├── cpang_fig1.pdf │ ├── cpang_fig2.pdf │ ├── cpang_fig3.pdf │ ├── phylogeny_and_vg.pdf │ └── vg_tubemap.pdf └── chapter1.tex ├── Chapter2 ├── Figs │ ├── DBG_to_GCSA.pdf │ ├── Variant calling on the graph [Page 1].pdf │ ├── Variant calling on the graph [Page 2].pdf │ ├── alignchain_dag.pdf │ ├── example_vg_construction.pdf │ ├── gbwt-example.pdf │ ├── loopy_dagify0.pdf │ ├── loopy_dagify1.pdf │ ├── loopy_dagify10.pdf │ ├── loopy_dagify17.pdf │ ├── loopy_dagify25.pdf │ ├── loopy_dagify4.pdf │ ├── mapping_cactus_pacbio_aln_viz.pdf │ ├── mapping_cactus_pacbio_aln_vizzy.pdf │ ├── mem-finding.pdf │ ├── memchain_dag.pdf │ ├── mississippi_bwt_construction.pdf │ ├── mississippi_iss_search.pdf │ ├── mississippi_suffix_tree.pdf │ ├── sdbg_construction.pdf │ ├── sequence_graph_to_DBG.pdf │ ├── vg_call.pdf │ ├── vg_genotype.pdf │ ├── vg_view_H-3136_Bandage.pdf │ ├── vg_view_dpS_H-3136_neato.pdf │ ├── vg_view_dp_H-3136_dot.pdf │ ├── vg_viz_H-3136.pdf │ ├── xbw_viz.pdf │ ├── xdrop.pdf │ ├── xdrop.png │ ├── xg_index_sketch.pdf │ └── xg_index_sketch_nice.pdf └── chapter2.tex ├── Chapter3 ├── Figs │ ├── ENCFF486KYD_AO_vg_pan_vs_bwa.png │ ├── ENCFF486KYD_RO_vg_pan_vs_bwa.png │ ├── ERR414817_holdout_bwa_vs_vg_k51_m3.png │ ├── HG002_wg_pan_ref_bwa_true_hets_allele_balance_tsv_gz_3.pdf │ ├── MHC_vg-msga_v1_9_0-115-gc20e80f_gfa.png │ ├── NA19240_hg38_vs_HGSVC_hist.png │ ├── NA19240_hg38_vs_HGSVC_scatter.png │ ├── NA24385_hg38_vs_HGSVC_hist.png │ ├── NA24385_hg38_vs_HGSVC_scatter.png │ ├── NCYC_SGRP2_SGD_comparison_id.png │ ├── NCYC_SGRP2_SGD_comparison_id_hist_color.pdf │ ├── NCYC_SGRP2_SGD_comparison_score.png │ ├── NCYC_SGRP2_SGD_comparison_score_hist_color.pdf │ ├── SRR2069949_100k_ref_vs_gene_model.png │ ├── SRS105153_k51a3_contigs_gfa.png │ ├── aDNA_d_stats_absolute.pdf │ ├── aDNA_d_stats_z_score.pdf │ ├── aDNA_downsampling.pdf │ ├── bwa_vs_vg_ancient_data_simulations_120218.pdf │ ├── bwa_vs_vg_ancient_data_simulations_mq30_recolored.pdf │ ├── cactus_yeast.png │ ├── cactus_yeast_zoom.pdf │ ├── compare-msga_dropSK1_vs_S288c.png │ ├── e68fc338_test_sim_yeast_cactus-roc.pdf │ ├── ecoli_10strain_cov_col_pos_0_1M.png │ ├── ecoli_10strain_cov_col_pos_4400000_100k.png │ ├── ecoli_10strain_kmer51abund10_contigs_vg_gfa.png │ ├── ecoli_cov_strains_hist.pdf │ ├── ecoli_n213909_c100.pdf │ ├── ecoli_n298051_c100.pdf │ ├── ecoli_pangenome_alignment_rate_vs_depth.pdf │ ├── human-10M-results-7358a67_merge_panel_labeled.pdf │ ├── human_gut_microbiome_SRS105153_holdout_vg_vs_bwa_scatter.png │ ├── human_gut_microbiome_phyla_colored_full_between.png │ ├── montage_vs_S288c_3x2.png │ ├── raw_viral_metagenome_zoom.png │ ├── seqwish_GI568335954_GI568335994_dotplot.png │ ├── seqwish_MHC.png │ ├── seqwish_MHC_n353767_neato.pdf │ ├── seqwish_MHC_n492324_viz.pdf │ ├── smoothed_viral_metagenome_zoom.png │ ├── svalbard_metagenome_minia_k51_m3_contigs_gfa.png │ ├── vg_msga_GI568335954_GI568335994_dotplot.png │ ├── vg_msga_yeast.png │ ├── yamna_1000GP_AB_het_hist.pdf │ └── yamna_1000GP_AB_het_violin.pdf └── chapter3.tex ├── Chapter4 └── chapter4.tex ├── Classes ├── PhDThesisPSnPDF.cls └── glyphtounicode.tex ├── Declaration └── declaration.tex ├── Dedication └── dedication.tex ├── Figs ├── CollegeShields │ ├── Fitzwilliam.eps │ ├── Fitzwilliam.pdf │ ├── FitzwilliamRed.eps │ ├── FitzwilliamRed.pdf │ ├── Gonville_and_Caius.jpg │ ├── Kings.eps │ ├── Kings.pdf │ ├── Licenses.md │ ├── Peterhouse.pdf │ ├── Queens.eps │ ├── Queens.pdf │ ├── StJohns.eps │ ├── StJohns.pdf │ ├── Trinity.eps │ ├── Trinity.pdf │ └── src │ │ ├── Kings.svg │ │ ├── Peterhouse.svg │ │ ├── Queens.svg │ │ └── Trinity.svg ├── University_Crest.eps ├── University_Crest.pdf ├── University_Crest_Long.eps └── University_Crest_Long.pdf ├── LICENSE ├── Makefile ├── Preamble └── preamble.tex ├── README.md ├── References └── references.bib ├── TODO.md ├── Variables.ini ├── compile-thesis-windows.bat ├── compile-thesis.sh ├── corrections_EG.pdf ├── license.md ├── sty └── breakurl.sty ├── thesis-info.tex ├── thesis-template-README.md └── thesis.tex /.gitignore: -------------------------------------------------------------------------------- 1 | *~ 2 | -------------------------------------------------------------------------------- /Abstract/abstract.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Abstract/abstract.tex -------------------------------------------------------------------------------- /Acknowledgement/acknowledgement.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Acknowledgement/acknowledgement.tex -------------------------------------------------------------------------------- /Appendix1/appendix1.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Appendix1/appendix1.tex -------------------------------------------------------------------------------- /Appendix2/appendix2.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Appendix2/appendix2.tex -------------------------------------------------------------------------------- /ChangeLog.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/ChangeLog.md -------------------------------------------------------------------------------- /Chapter1/Figs/cpang_fig1.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter1/Figs/cpang_fig1.pdf -------------------------------------------------------------------------------- /Chapter1/Figs/cpang_fig2.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter1/Figs/cpang_fig2.pdf -------------------------------------------------------------------------------- /Chapter1/Figs/cpang_fig3.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter1/Figs/cpang_fig3.pdf -------------------------------------------------------------------------------- /Chapter1/Figs/phylogeny_and_vg.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter1/Figs/phylogeny_and_vg.pdf -------------------------------------------------------------------------------- /Chapter1/Figs/vg_tubemap.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter1/Figs/vg_tubemap.pdf -------------------------------------------------------------------------------- /Chapter1/chapter1.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter1/chapter1.tex -------------------------------------------------------------------------------- /Chapter2/Figs/DBG_to_GCSA.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/DBG_to_GCSA.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/Variant calling on the graph [Page 1].pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/Variant calling on the graph [Page 1].pdf -------------------------------------------------------------------------------- /Chapter2/Figs/Variant calling on the graph [Page 2].pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/Variant calling on the graph [Page 2].pdf -------------------------------------------------------------------------------- /Chapter2/Figs/alignchain_dag.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/alignchain_dag.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/example_vg_construction.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/example_vg_construction.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/gbwt-example.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/gbwt-example.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/loopy_dagify0.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/loopy_dagify0.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/loopy_dagify1.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/loopy_dagify1.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/loopy_dagify10.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/loopy_dagify10.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/loopy_dagify17.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/loopy_dagify17.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/loopy_dagify25.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/loopy_dagify25.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/loopy_dagify4.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/loopy_dagify4.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/mapping_cactus_pacbio_aln_viz.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/mapping_cactus_pacbio_aln_viz.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/mapping_cactus_pacbio_aln_vizzy.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/mapping_cactus_pacbio_aln_vizzy.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/mem-finding.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/mem-finding.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/memchain_dag.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/memchain_dag.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/mississippi_bwt_construction.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/mississippi_bwt_construction.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/mississippi_iss_search.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/mississippi_iss_search.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/mississippi_suffix_tree.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/mississippi_suffix_tree.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/sdbg_construction.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/sdbg_construction.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/sequence_graph_to_DBG.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/sequence_graph_to_DBG.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/vg_call.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/vg_call.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/vg_genotype.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/vg_genotype.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/vg_view_H-3136_Bandage.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/vg_view_H-3136_Bandage.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/vg_view_dpS_H-3136_neato.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/vg_view_dpS_H-3136_neato.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/vg_view_dp_H-3136_dot.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/vg_view_dp_H-3136_dot.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/vg_viz_H-3136.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/vg_viz_H-3136.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/xbw_viz.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/xbw_viz.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/xdrop.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/xdrop.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/xdrop.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/xdrop.png -------------------------------------------------------------------------------- /Chapter2/Figs/xg_index_sketch.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/xg_index_sketch.pdf -------------------------------------------------------------------------------- /Chapter2/Figs/xg_index_sketch_nice.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/Figs/xg_index_sketch_nice.pdf -------------------------------------------------------------------------------- /Chapter2/chapter2.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter2/chapter2.tex -------------------------------------------------------------------------------- /Chapter3/Figs/ENCFF486KYD_AO_vg_pan_vs_bwa.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/ENCFF486KYD_AO_vg_pan_vs_bwa.png -------------------------------------------------------------------------------- /Chapter3/Figs/ENCFF486KYD_RO_vg_pan_vs_bwa.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/ENCFF486KYD_RO_vg_pan_vs_bwa.png -------------------------------------------------------------------------------- /Chapter3/Figs/ERR414817_holdout_bwa_vs_vg_k51_m3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/ERR414817_holdout_bwa_vs_vg_k51_m3.png -------------------------------------------------------------------------------- /Chapter3/Figs/HG002_wg_pan_ref_bwa_true_hets_allele_balance_tsv_gz_3.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/HG002_wg_pan_ref_bwa_true_hets_allele_balance_tsv_gz_3.pdf -------------------------------------------------------------------------------- /Chapter3/Figs/MHC_vg-msga_v1_9_0-115-gc20e80f_gfa.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/MHC_vg-msga_v1_9_0-115-gc20e80f_gfa.png -------------------------------------------------------------------------------- /Chapter3/Figs/NA19240_hg38_vs_HGSVC_hist.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/NA19240_hg38_vs_HGSVC_hist.png -------------------------------------------------------------------------------- /Chapter3/Figs/NA19240_hg38_vs_HGSVC_scatter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/NA19240_hg38_vs_HGSVC_scatter.png -------------------------------------------------------------------------------- /Chapter3/Figs/NA24385_hg38_vs_HGSVC_hist.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/NA24385_hg38_vs_HGSVC_hist.png -------------------------------------------------------------------------------- /Chapter3/Figs/NA24385_hg38_vs_HGSVC_scatter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/NA24385_hg38_vs_HGSVC_scatter.png -------------------------------------------------------------------------------- /Chapter3/Figs/NCYC_SGRP2_SGD_comparison_id.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/NCYC_SGRP2_SGD_comparison_id.png -------------------------------------------------------------------------------- /Chapter3/Figs/NCYC_SGRP2_SGD_comparison_id_hist_color.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/NCYC_SGRP2_SGD_comparison_id_hist_color.pdf -------------------------------------------------------------------------------- /Chapter3/Figs/NCYC_SGRP2_SGD_comparison_score.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/NCYC_SGRP2_SGD_comparison_score.png -------------------------------------------------------------------------------- /Chapter3/Figs/NCYC_SGRP2_SGD_comparison_score_hist_color.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/NCYC_SGRP2_SGD_comparison_score_hist_color.pdf -------------------------------------------------------------------------------- /Chapter3/Figs/SRR2069949_100k_ref_vs_gene_model.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/SRR2069949_100k_ref_vs_gene_model.png -------------------------------------------------------------------------------- /Chapter3/Figs/SRS105153_k51a3_contigs_gfa.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/SRS105153_k51a3_contigs_gfa.png -------------------------------------------------------------------------------- /Chapter3/Figs/aDNA_d_stats_absolute.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/aDNA_d_stats_absolute.pdf -------------------------------------------------------------------------------- /Chapter3/Figs/aDNA_d_stats_z_score.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/aDNA_d_stats_z_score.pdf -------------------------------------------------------------------------------- /Chapter3/Figs/aDNA_downsampling.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/aDNA_downsampling.pdf -------------------------------------------------------------------------------- /Chapter3/Figs/bwa_vs_vg_ancient_data_simulations_120218.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/bwa_vs_vg_ancient_data_simulations_120218.pdf -------------------------------------------------------------------------------- /Chapter3/Figs/bwa_vs_vg_ancient_data_simulations_mq30_recolored.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/bwa_vs_vg_ancient_data_simulations_mq30_recolored.pdf -------------------------------------------------------------------------------- /Chapter3/Figs/cactus_yeast.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/cactus_yeast.png -------------------------------------------------------------------------------- /Chapter3/Figs/cactus_yeast_zoom.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/cactus_yeast_zoom.pdf -------------------------------------------------------------------------------- /Chapter3/Figs/compare-msga_dropSK1_vs_S288c.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/compare-msga_dropSK1_vs_S288c.png -------------------------------------------------------------------------------- /Chapter3/Figs/e68fc338_test_sim_yeast_cactus-roc.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/e68fc338_test_sim_yeast_cactus-roc.pdf -------------------------------------------------------------------------------- /Chapter3/Figs/ecoli_10strain_cov_col_pos_0_1M.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/ecoli_10strain_cov_col_pos_0_1M.png -------------------------------------------------------------------------------- /Chapter3/Figs/ecoli_10strain_cov_col_pos_4400000_100k.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/ecoli_10strain_cov_col_pos_4400000_100k.png -------------------------------------------------------------------------------- /Chapter3/Figs/ecoli_10strain_kmer51abund10_contigs_vg_gfa.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/ecoli_10strain_kmer51abund10_contigs_vg_gfa.png -------------------------------------------------------------------------------- /Chapter3/Figs/ecoli_cov_strains_hist.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/ecoli_cov_strains_hist.pdf -------------------------------------------------------------------------------- /Chapter3/Figs/ecoli_n213909_c100.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/ecoli_n213909_c100.pdf -------------------------------------------------------------------------------- /Chapter3/Figs/ecoli_n298051_c100.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/ecoli_n298051_c100.pdf -------------------------------------------------------------------------------- /Chapter3/Figs/ecoli_pangenome_alignment_rate_vs_depth.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/ecoli_pangenome_alignment_rate_vs_depth.pdf -------------------------------------------------------------------------------- /Chapter3/Figs/human-10M-results-7358a67_merge_panel_labeled.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/human-10M-results-7358a67_merge_panel_labeled.pdf -------------------------------------------------------------------------------- /Chapter3/Figs/human_gut_microbiome_SRS105153_holdout_vg_vs_bwa_scatter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/human_gut_microbiome_SRS105153_holdout_vg_vs_bwa_scatter.png -------------------------------------------------------------------------------- /Chapter3/Figs/human_gut_microbiome_phyla_colored_full_between.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/human_gut_microbiome_phyla_colored_full_between.png -------------------------------------------------------------------------------- /Chapter3/Figs/montage_vs_S288c_3x2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/montage_vs_S288c_3x2.png -------------------------------------------------------------------------------- /Chapter3/Figs/raw_viral_metagenome_zoom.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/raw_viral_metagenome_zoom.png -------------------------------------------------------------------------------- /Chapter3/Figs/seqwish_GI568335954_GI568335994_dotplot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/seqwish_GI568335954_GI568335994_dotplot.png -------------------------------------------------------------------------------- /Chapter3/Figs/seqwish_MHC.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/seqwish_MHC.png -------------------------------------------------------------------------------- /Chapter3/Figs/seqwish_MHC_n353767_neato.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/seqwish_MHC_n353767_neato.pdf -------------------------------------------------------------------------------- /Chapter3/Figs/seqwish_MHC_n492324_viz.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/seqwish_MHC_n492324_viz.pdf -------------------------------------------------------------------------------- /Chapter3/Figs/smoothed_viral_metagenome_zoom.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/smoothed_viral_metagenome_zoom.png -------------------------------------------------------------------------------- /Chapter3/Figs/svalbard_metagenome_minia_k51_m3_contigs_gfa.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/svalbard_metagenome_minia_k51_m3_contigs_gfa.png -------------------------------------------------------------------------------- /Chapter3/Figs/vg_msga_GI568335954_GI568335994_dotplot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/vg_msga_GI568335954_GI568335994_dotplot.png -------------------------------------------------------------------------------- /Chapter3/Figs/vg_msga_yeast.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/vg_msga_yeast.png -------------------------------------------------------------------------------- /Chapter3/Figs/yamna_1000GP_AB_het_hist.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/yamna_1000GP_AB_het_hist.pdf -------------------------------------------------------------------------------- /Chapter3/Figs/yamna_1000GP_AB_het_violin.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/Figs/yamna_1000GP_AB_het_violin.pdf -------------------------------------------------------------------------------- /Chapter3/chapter3.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter3/chapter3.tex -------------------------------------------------------------------------------- /Chapter4/chapter4.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Chapter4/chapter4.tex -------------------------------------------------------------------------------- /Classes/PhDThesisPSnPDF.cls: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Classes/PhDThesisPSnPDF.cls -------------------------------------------------------------------------------- /Classes/glyphtounicode.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Classes/glyphtounicode.tex -------------------------------------------------------------------------------- /Declaration/declaration.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Declaration/declaration.tex -------------------------------------------------------------------------------- /Dedication/dedication.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Dedication/dedication.tex -------------------------------------------------------------------------------- /Figs/CollegeShields/Fitzwilliam.eps: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/CollegeShields/Fitzwilliam.eps -------------------------------------------------------------------------------- /Figs/CollegeShields/Fitzwilliam.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/CollegeShields/Fitzwilliam.pdf -------------------------------------------------------------------------------- /Figs/CollegeShields/FitzwilliamRed.eps: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/CollegeShields/FitzwilliamRed.eps -------------------------------------------------------------------------------- /Figs/CollegeShields/FitzwilliamRed.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/CollegeShields/FitzwilliamRed.pdf -------------------------------------------------------------------------------- /Figs/CollegeShields/Gonville_and_Caius.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/CollegeShields/Gonville_and_Caius.jpg -------------------------------------------------------------------------------- /Figs/CollegeShields/Kings.eps: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/CollegeShields/Kings.eps -------------------------------------------------------------------------------- /Figs/CollegeShields/Kings.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/CollegeShields/Kings.pdf -------------------------------------------------------------------------------- /Figs/CollegeShields/Licenses.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/CollegeShields/Licenses.md -------------------------------------------------------------------------------- /Figs/CollegeShields/Peterhouse.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/CollegeShields/Peterhouse.pdf -------------------------------------------------------------------------------- /Figs/CollegeShields/Queens.eps: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/CollegeShields/Queens.eps -------------------------------------------------------------------------------- /Figs/CollegeShields/Queens.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/CollegeShields/Queens.pdf -------------------------------------------------------------------------------- /Figs/CollegeShields/StJohns.eps: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/CollegeShields/StJohns.eps -------------------------------------------------------------------------------- /Figs/CollegeShields/StJohns.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/CollegeShields/StJohns.pdf -------------------------------------------------------------------------------- /Figs/CollegeShields/Trinity.eps: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/CollegeShields/Trinity.eps -------------------------------------------------------------------------------- /Figs/CollegeShields/Trinity.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/CollegeShields/Trinity.pdf -------------------------------------------------------------------------------- /Figs/CollegeShields/src/Kings.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/CollegeShields/src/Kings.svg -------------------------------------------------------------------------------- /Figs/CollegeShields/src/Peterhouse.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/CollegeShields/src/Peterhouse.svg -------------------------------------------------------------------------------- /Figs/CollegeShields/src/Queens.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/CollegeShields/src/Queens.svg -------------------------------------------------------------------------------- /Figs/CollegeShields/src/Trinity.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/CollegeShields/src/Trinity.svg -------------------------------------------------------------------------------- /Figs/University_Crest.eps: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/University_Crest.eps -------------------------------------------------------------------------------- /Figs/University_Crest.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/University_Crest.pdf -------------------------------------------------------------------------------- /Figs/University_Crest_Long.eps: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/University_Crest_Long.eps -------------------------------------------------------------------------------- /Figs/University_Crest_Long.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Figs/University_Crest_Long.pdf -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/LICENSE -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Makefile -------------------------------------------------------------------------------- /Preamble/preamble.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Preamble/preamble.tex -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/README.md -------------------------------------------------------------------------------- /References/references.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/References/references.bib -------------------------------------------------------------------------------- /TODO.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/TODO.md -------------------------------------------------------------------------------- /Variables.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/Variables.ini -------------------------------------------------------------------------------- /compile-thesis-windows.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/compile-thesis-windows.bat -------------------------------------------------------------------------------- /compile-thesis.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/compile-thesis.sh -------------------------------------------------------------------------------- /corrections_EG.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/corrections_EG.pdf -------------------------------------------------------------------------------- /license.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/license.md -------------------------------------------------------------------------------- /sty/breakurl.sty: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/sty/breakurl.sty -------------------------------------------------------------------------------- /thesis-info.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/thesis-info.tex -------------------------------------------------------------------------------- /thesis-template-README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/thesis-template-README.md -------------------------------------------------------------------------------- /thesis.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ekg/thesis/HEAD/thesis.tex --------------------------------------------------------------------------------