quanrd/thesis

my PhD thesis

Graphical pangenomics

100-150 pages, ~25k words

Outline annotated with expected effort and length:

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introduction

0.5p 1.5h

review of reference sequence literature

0.5p 1h

brief retrospective on DNA sequencing and references

2p 3h

the reference bias problem

2p 2h

alt-aware references and their limits

2p 3h

review of uses of graphs in sequence analysis

0.5p 0.5h

MSAs

1p 1h

assembly graphs

3p 3h

overlap assembly graphs

debruijn graphs (colored in particular)

RNA splicing graphs

1p 1h

variant representation (VCF encodes a DAG)

0.5p 0.5h

the variation graph

1p 1h

data models

0.5p 1h

the graph itself

1p 1h

edits to the graph

1p 1h

alignments and translations

1p 1h

bubbles and variant calls

2p 2.5h

graph construction

0.5p 0.5h

progressively (vg msga)

1p 1h

from variants (VCF)

1.5p 1h

from gene models (GFF)

1p 4h

from MSAs

0.5p 0.5h

from overlap graphs (assemblies)

2p 1.5h

from pairwise alignments

2p 4h

from other sources (e.g.g cactus)

0.5p 0.5h

index structures

0.5p 0.5h

XG index

2p 3h

GCSA2 index

1p 2h

haplotype indexes

1.5p 2h

generic disk backed indexes

0.5p 0.5h

coverage index

1p 1h

local and global alignment

0.5p 0.5h

POA and GSSW

2p 2h

banded global alignment

0.5p 0.5h

MEM finding

2p 2h

X-drop DP

0.5p 0.5h

collinear chaining

0.5p 0.5h

distance estimation

1p 1h

MEM chaining

2.5p 3h

chunked alignment

1p 1h

finding the alignment

0.5p 0.5h

surjection

1p 1h

mapping quality

2p 2h

visualization

0.5p 0.5h

hierarchical layout

0.5p 0.5h

force directed models

1p 1.5h

linear time visualization

1p 2h

graph mutating algorithms

0.5p 0.5h

edit

1p 1h

pruning

2.5p 3h

sort

1p 1h

simplification

0.5p 0.5h

graphs as basis spaces for sequence data

2p 2h

coverage maps

1p 1h

variant calling

3p 2h

bubble decompositions and likelihood spaces

2p 4h

MEM matching to the bidirectional GBWT

1p 3h

applications

0.5p 1h

yeast

0.5p 0.5h

a SNP-based SGRP2 graph

1p 1h

cactus progressive assembly

0.5p 0.5h

constructing and comparing variation graphs from whole genome assemblies

3p 2.5h

human

0.5p 0.5h

1000GP graph construction and indexing

1.5p 1h

simulations based on phased HG002

2p 2.5h

whole genome variant calling experiments

1p 2h

HGSVC from VCF and progressive alignment of human chromosomes

2.5p 5h

aDNA

0.5p 0.5h

simulations with human origins panel

1p 2h

using 1000GP graph for samples from Martiniano et al 2016

2p 4h

evaluation of a high-coverage Botai sample

2p 4h

neoclassical bacterial pangenomics

0.5p 0.5h

e. coli pangenome from illumina reads

2p 4h

evaluating the core and accessory pangenome

2p 4h

metagenomics

0.5p 0.5h

arctic viral metagenome

2p 1.5h

human gut microbiome

2p 4h

RNAseq

0.5p 0.5h

yeast

1p 2h

nematode

2p 5h

human

2p 6h

discussion and conclusion

3p 4h

vg in the context of modern sequence analysis

2p 1.5h

limitations of current approaches

2p 2h

next steps

4p 5h