Pan-genomics in the human genome era
RM Sherman, SL Salzberg - Nature Reviews Genetics, 2020 - nature.com
Since the early days of the genome era, the scientific community has relied on a single
'reference'genome for each species, which is used as the basis for a wide range of genetic …
'reference'genome for each species, which is used as the basis for a wide range of genetic …
Pangenome graphs
JM Eizenga, AM Novak, JA Sibbesen… - Annual review of …, 2020 - annualreviews.org
Low-cost whole-genome assembly has enabled the collection of haplotype-resolved
pangenomes for numerous organisms. In turn, this technological change is encouraging the …
pangenomes for numerous organisms. In turn, this technological change is encouraging the …
Variation graph toolkit improves read mapping by representing genetic variation in the reference
Reference genomes guide our interpretation of DNA sequence data. However, conventional
linear references represent only one version of each locus, ignoring variation in the …
linear references represent only one version of each locus, ignoring variation in the …
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
VA Schneider, T Graves-Lindsay, K Howe… - Genome …, 2017 - genome.cshlp.org
The human reference genome assembly plays a central role in nearly all aspects of today's
basic and clinical research. GRCh38 is the first coordinate-changing assembly update since …
basic and clinical research. GRCh38 is the first coordinate-changing assembly update since …
Genome graphs and the evolution of genome inference
The human reference genome is part of the foundation of modern human biology and a
monumental scientific achievement. However, because it excludes a great deal of common …
monumental scientific achievement. However, because it excludes a great deal of common …
Fast and accurate genomic analyses using genome graphs
The human reference genome serves as the foundation for genomics by providing a scaffold
for alignment of sequencing reads, but currently only reflects a single consensus haplotype …
for alignment of sequencing reads, but currently only reflects a single consensus haplotype …
[HTML][HTML] Wheeler graphs: A framework for BWT-based data structures
Abstract The famous Burrows–Wheeler Transform (BWT) was originally defined for a single
string but variations have been developed for sets of strings, labeled trees, de Bruijn graphs …
string but variations have been developed for sets of strings, labeled trees, de Bruijn graphs …
Computational graph pangenomics: a tutorial on data structures and their applications
Computational pangenomics is an emerging research field that is changing the way
computer scientists are facing challenges in biological sequence analysis. In past decades …
computer scientists are facing challenges in biological sequence analysis. In past decades …
Exploring pan-genomes: an overview of resources and tools for unraveling structure, function, and evolution of crop genes and genomes
The availability of multiple sequenced genomes from a single species made it possible to
explore intra-and inter-specific genomic comparisons at higher resolution and build clade …
explore intra-and inter-specific genomic comparisons at higher resolution and build clade …
Haplotype-aware graph indexes
Motivation The variation graph toolkit (VG) represents genetic variation as a graph. Although
each path in the graph is a potential haplotype, most paths are non-biological, unlikely …
each path in the graph is a potential haplotype, most paths are non-biological, unlikely …