[HTML][HTML] Nanopore sequencing technology, bioinformatics and applications
Rapid advances in nanopore technologies for sequencing single long DNA and RNA
molecules have led to substantial improvements in accuracy, read length and throughput …
molecules have led to substantial improvements in accuracy, read length and throughput …
Twenty years of plant genome sequencing: achievements and challenges
Y Sun, L Shang, QH Zhu, L Fan, L Guo - Trends in Plant Science, 2022 - cell.com
Publication of the complete genome sequence of Arabidopsis thaliana, the first plant
reference genome, in December 2000 heralded the beginning of the plant genome era …
reference genome, in December 2000 heralded the beginning of the plant genome era …
Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits
Y Huang, J He, Y Xu, W Zheng, S Wang, P Chen… - Nature …, 2023 - nature.com
The orange subfamily (Aurantioideae) contains several Citrus species cultivated worldwide,
such as sweet orange and lemon. The origin of Citrus species has long been debated and …
such as sweet orange and lemon. The origin of Citrus species has long been debated and …
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence
variations in a genome. However, existing algorithms either collapse heterozygous alleles …
variations in a genome. However, existing algorithms either collapse heterozygous alleles …
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 …
NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads
Long-read sequencing data, particularly those derived from the Oxford Nanopore
sequencing platform, tend to exhibit high error rates. Here, we present NextDenovo, an …
sequencing platform, tend to exhibit high error rates. Here, we present NextDenovo, an …
Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing
A perfect bacterial genome assembly is one where the assembled sequence is an exact
match for the organism's genome—each replicon sequence is complete and contains no …
match for the organism's genome—each replicon sequence is complete and contains no …
Benchmarking of long-read assemblers for prokaryote whole genome sequencing
Background: Data sets from long-read sequencing platforms (Oxford Nanopore
Technologies and Pacific Biosciences) allow for most prokaryote genomes to be completely …
Technologies and Pacific Biosciences) allow for most prokaryote genomes to be completely …
The integrated genomics of crop domestication and breeding
X Huang, S Huang, B Han, J Li - Cell, 2022 - cell.com
As a major event in human civilization, wild plants were successfully domesticated to be
crops, largely owing to continuing artificial selection. Here, we summarize new discoveries …
crops, largely owing to continuing artificial selection. Here, we summarize new discoveries …
[HTML][HTML] A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data
Metagenomic sequencing provides a culture-independent avenue to investigate the
complex microbial communities by constructing metagenome-assembled genomes (MAGs) …
complex microbial communities by constructing metagenome-assembled genomes (MAGs) …