Long reads: their purpose and place
In recent years long-read technologies have moved from being a niche and specialist field to
a point of relative maturity likely to feature frequently in the genomic landscape. Analogous …
a point of relative maturity likely to feature frequently in the genomic landscape. Analogous …
The need for a human pangenome reference sequence
The reference human genome sequence is inarguably the most important and widely used
resource in the fields of human genetics and genomics. It has transformed the conduct of …
resource in the fields of human genetics and genomics. It has transformed the conduct of …
The crucial role of genome-wide genetic variation in conservation
The unprecedented rate of extinction calls for efficient use of genetics to help conserve
biodiversity. Several recent genomic and simulation-based studies have argued that the …
biodiversity. Several recent genomic and simulation-based studies have argued that the …
Long-read map** to repetitive reference sequences using Winnowmap2
Abstract Approximately 5–10% of the human genome remains inaccessible due to the
presence of repetitive sequences such as segmental duplications and tandem repeat arrays …
presence of repetitive sequences such as segmental duplications and tandem repeat arrays …
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
De novo assembly of a human genome using nanopore long-read sequences has been
reported, but it used more than 150,000 CPU hours and weeks of wall-clock time. To enable …
reported, but it used more than 150,000 CPU hours and weeks of wall-clock time. To enable …
TGS-GapCloser: a fast and accurate gap closer for large genomes with low coverage of error-prone long reads
Background Analyses that use genome assemblies are critically affected by the contiguity,
completeness, and accuracy of those assemblies. In recent years single-molecule …
completeness, and accuracy of those assemblies. In recent years single-molecule …
[HTML][HTML] Characterizing the major structural variant alleles of the human genome
In order to provide a comprehensive resource for human structural variants (SVs), we
generated long-read sequence data and analyzed SVs for fifteen human genomes. We …
generated long-read sequence data and analyzed SVs for fifteen human genomes. We …
Map** and phasing of structural variation in patient genomes using nanopore sequencing
M Cretu Stancu, MJ Van Roosmalen, I Renkens… - Nature …, 2017 - nature.com
Despite improvements in genomics technology, the detection of structural variants (SVs)
from short-read sequencing still poses challenges, particularly for complex variation. Here …
from short-read sequencing still poses challenges, particularly for complex variation. Here …
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 …
The presence and impact of reference bias on population genomic studies of prehistoric human populations
Haploid high quality reference genomes are an important resource in genomic research
projects. A consequence is that DNA fragments carrying the reference allele will be more …
projects. A consequence is that DNA fragments carrying the reference allele will be more …