Long-read human genome sequencing and its applications
Over the past decade, long-read, single-molecule DNA sequencing technologies have
emerged as powerful players in genomics. With the ability to generate reads tens to …
emerged as powerful players in genomics. With the ability to generate reads tens to …
Sequencing and characterizing short tandem repeats in the human genome
HA Tanudisastro, IW Deveson, H Dashnow… - Nature Reviews …, 2024 - nature.com
Short tandem repeats (STRs) are highly polymorphic sequences throughout the human
genome that are composed of repeated copies of a 1–6-bp motif. Over 1 million variable …
genome that are composed of repeated copies of a 1–6-bp motif. Over 1 million variable …
Haplotype-resolved assembly of diploid genomes without parental data
Routine haplotype-resolved genome assembly from single samples remains an unresolved
problem. Here we describe an algorithm that combines PacBio HiFi reads and Hi-C …
problem. Here we describe an algorithm that combines PacBio HiFi reads and Hi-C …
Towards complete and error-free genome assemblies of all vertebrate species
High-quality and complete reference genome assemblies are fundamental for the
application of genomics to biology, disease, and biodiversity conservation. However, such …
application of genomics to biology, disease, and biodiversity conservation. However, such …
Semi-automated assembly of high-quality diploid human reference genomes
The current human reference genome, GRCh38, represents over 20 years of effort to
generate a high-quality assembly, which has benefitted society,. However, it still has many …
generate a high-quality assembly, which has benefitted society,. However, it still has many …
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
Recent long-read assemblies often exceed the quality and completeness of available
reference genomes, making validation challenging. Here we present Merqury, a novel tool …
reference genomes, making validation challenging. Here we present Merqury, a novel tool …
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
Complete and accurate genome assemblies form the basis of most downstream genomic
analyses and are of critical importance. Recent genome assembly projects have relied on a …
analyses and are of critical importance. Recent genome assembly projects have relied on a …
Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
Human genomes are typically assembled as consensus sequences that lack information on
parental haplotypes. Here we describe a reference-free workflow for diploid de novo …
parental haplotypes. Here we describe a reference-free workflow for diploid de novo …
Centuries of genome instability and evolution in soft-shell clam, Mya arenaria, bivalve transmissible neoplasia
SFM Hart, MA Yonemitsu, RM Giersch, FES Garrett… - Nature Cancer, 2023 - nature.com
Transmissible cancers are infectious parasitic clones that metastasize to new hosts, living
past the death of the founder animal in which the cancer initiated. We investigated the …
past the death of the founder animal in which the cancer initiated. We investigated the …
Chromosome-scale, haplotype-resolved assembly of human genomes
Haplotype-resolved or phased genome assembly provides a complete picture of genomes
and their complex genetic variations. However, current algorithms for phased assembly …
and their complex genetic variations. However, current algorithms for phased assembly …