Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics
S Ardui, A Ameur, JR Vermeesch… - Nucleic acids …, 2018 - academic.oup.com
Short read massive parallel sequencing has emerged as a standard diagnostic tool in the
medical setting. However, short read technologies have inherent limitations such as GC …
medical setting. However, short read technologies have inherent limitations such as GC …
Piercing the dark matter: bioinformatics of long-range sequencing and mapping
Several new genomics technologies have become available that offer long-read sequencing
or long-range mapping with higher throughput and higher resolution analysis than ever …
or long-range mapping with higher throughput and higher resolution analysis than ever …
Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads
Long-read sequencing has the potential to transform variant detection by reaching currently
difficult-to-map regions and routinely linking together adjacent variations to enable read …
difficult-to-map regions and routinely linking together adjacent variations to enable read …
Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics
NC Rochette, AG Rivera‐Colón… - Molecular ecology, 2019 - Wiley Online Library
For half a century population genetics studies have put type II restriction endonucleases to
work. Now, coupled with massively‐parallel, short‐read sequencing, the family of RAD …
work. Now, coupled with massively‐parallel, short‐read sequencing, the family of RAD …
3D genomics across the tree of life reveals condensin II as a determinant of architecture type
C Hoencamp, O Dudchenko, AMO Elbatsh… - Science, 2021 - science.org
We investigated genome folding across the eukaryotic tree of life. We find two types of three-
dimensional (3D) genome architectures at the chromosome scale. Each type appears and …
dimensional (3D) genome architectures at the chromosome scale. Each type appears and …
Accurate, scalable and integrative haplotype estimation
O Delaneau, JF Zagury, MR Robinson… - Nature …, 2019 - nature.com
The number of human genomes being genotyped or sequenced increases exponentially
and efficient haplotype estimation methods able to handle this amount of data are now …
and efficient haplotype estimation methods able to handle this amount of data are now …
Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits
BC Zhang, A Biddanda, ÁF Gunnarsson, F Cooper… - Nature Genetics, 2023 - nature.com
Genome-wide genealogies compactly represent the evolutionary history of a set of genomes
and inferring them from genetic data has the potential to facilitate a wide range of analyses …
and inferring them from genetic data has the potential to facilitate a wide range of analyses …
Reference-based phasing using the Haplotype Reference Consortium panel
Haplotype phasing is a fundamental problem in medical and population genetics. Phasing is
generally performed via statistical phasing in a genotyped cohort, an approach that can yield …
generally performed via statistical phasing in a genotyped cohort, an approach that can yield …
Deriving genotypes from RAD-seq short-read data using Stacks
NC Rochette, JM Catchen - Nature protocols, 2017 - nature.com
Restriction site-associated DNA sequencing (RAD-seq) allows for the genome-wide
discovery and genotyping of single-nucleotide polymorphisms in hundreds of individuals at …
discovery and genotyping of single-nucleotide polymorphisms in hundreds of individuals at …
Robust and scalable inference of population history from hundreds of unphased whole genomes
J Terhorst, JA Kamm, YS Song - Nature genetics, 2017 - nature.com
It has recently been demonstrated that inference methods based on genealogical processes
with recombination can uncover past population history in unprecedented detail. However …
with recombination can uncover past population history in unprecedented detail. However …