New whole-genome alignment tools are needed for tapping into plant diversity
B Song, ES Buckler, MC Stitzer - Trends in Plant Science, 2024 - cell.com
Genome alignment is one of the most foundational methods for genome sequence studies.
With rapid advances in sequencing and assembly technologies, these newly assembled …
With rapid advances in sequencing and assembly technologies, these newly assembled …
The complete sequence of a human Y chromosome
The human Y chromosome has been notoriously difficult to sequence and assemble
because of its complex repeat structure that includes long palindromes, tandem repeats and …
because of its complex repeat structure that includes long palindromes, tandem repeats and …
A survey of mapping algorithms in the long-reads era
It has been over a decade since the first publication of a method dedicated entirely to
mapping long-reads. The distinctive characteristics of long reads resulted in methods …
mapping long-reads. The distinctive characteristics of long reads resulted in methods …
Building pangenome graphs
Pangenome graphs can represent all variation between multiple reference genomes, but
current approaches to build them exclude complex sequences or are based upon a single …
current approaches to build them exclude complex sequences or are based upon a single …
Long-read mapping 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 …
A modern primer on processing in memory
Modern computing systems are overwhelmingly designed to move data to computation. This
design choice goes directly against at least three key trends in computing that cause …
design choice goes directly against at least three key trends in computing that cause …
Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing
The year 2022 will be remembered as the turning point for accurate long-read sequencing,
which now establishes the gold standard for speed and accuracy at competitive costs. We …
which now establishes the gold standard for speed and accuracy at competitive costs. We …
High-quality metagenome assembly from long accurate reads with metaMDBG
We introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads. MetaMDBG
combines a de Bruijn graph assembly in a minimizer space with an iterative assembly over …
combines a de Bruijn graph assembly in a minimizer space with an iterative assembly over …
Recombination between heterologous human acrocentric chromosomes
The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share
large homologous regions, including ribosomal DNA repeats and extended segmental …
large homologous regions, including ribosomal DNA repeats and extended segmental …
High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
JA Gustafson, SB Gibson, N Damaraju… - Genome …, 2024 - genome.cshlp.org
Fewer than half of individuals with a suspected Mendelian or monogenic condition receive a
precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in …
precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in …