100-150 pages, ~25k words
Outline annotated with expected effort and length:
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
1p 1h
3p 3h
debruijn graphs (colored in particular)
1p 1h
variant representation (VCF encodes a DAG)
0.5p 0.5h
1p 1h
0.5p 1h
1p 1h
1p 1h
alignments and translations
1p 1h
bubbles and variant calls
2p 2.5h
0.5p 0.5h
1p 1h
1.5p 1h
1p 4h
0.5p 0.5h
from overlap graphs (assemblies)
2p 1.5h
2p 4h
from other sources (e.g.g cactus)
0.5p 0.5h
0.5p 0.5h
2p 3h
1p 2h
1.5p 2h
generic disk backed indexes
0.5p 0.5h
1p 1h
local and global alignment
0.5p 0.5h
2p 2h
0.5p 0.5h
2p 2h
0.5p 0.5h
0.5p 0.5h
1p 1h
2.5p 3h
1p 1h
0.5p 0.5h
1p 1h
2p 2h
0.5p 0.5h
0.5p 0.5h
1p 1.5h
linear time visualization
1p 2h
graph mutating algorithms
0.5p 0.5h
1p 1h
2.5p 3h
1p 1h
0.5p 0.5h
graphs as basis spaces for sequence data
2p 2h
1p 1h
3p 2h
bubble decompositions and likelihood spaces
2p 4h
MEM matching to the bidirectional GBWT
1p 3h
0.5p 1h
0.5p 0.5h
1p 1h
cactus progressive assembly
0.5p 0.5h
constructing and comparing variation graphs from whole genome assemblies
3p 2.5h
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
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
0.5p 0.5h
2p 1.5h
2p 4h
0.5p 0.5h
1p 2h
2p 5h
2p 6h
discussion and conclusion
3p 4h
vg in the context of modern sequence analysis
2p 1.5h
limitations of current approaches
2p 2h
4p 5h