Tools and strategies for long-read sequencing and de novo assembly of plant genomes
The commercial release of third-generation sequencing technologies (TGSTs), giving long
and ultra-long sequencing reads, has stimulated the development of new tools for …
and ultra-long sequencing reads, has stimulated the development of new tools for …
Highly accurate long-read HiFi sequencing data for five complex genomes
T Hon, K Mars, G Young, YC Tsai, JW Karalius… - Scientific data, 2020 - nature.com
Abstract The PacBio® HiFi sequencing method yields highly accurate long-read sequencing
datasets with read lengths averaging 10–25 kb and accuracies greater than 99.5%. These …
datasets with read lengths averaging 10–25 kb and accuracies greater than 99.5%. These …
[HTML][HTML] Ten steps to get started in Genome Assembly and Annotation
As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps
to facilitate researchers getting started in genome assembly and genome annotation. The …
to facilitate researchers getting started in genome assembly and genome annotation. The …
Trimming and validation of Illumina short reads using trimmomatic, trinity assembly, and assessment of RNA-seq data
SO Sewe, G Silva, P Sicat, SE Seal… - … : Methods and protocols, 2022 - Springer
Next-generation sequencing (NGS) technologies can generate billions of reads in a single
sequencing run. However, with such high-throughput comes quality issues which have to be …
sequencing run. However, with such high-throughput comes quality issues which have to be …
Molecular microbial community analysis as an analysis tool for optimal biogas production
The microbial diversity in anaerobic digestion (AD) is important because it affects process
robustness. High-throughput sequencing offers high-resolution data regarding the microbial …
robustness. High-throughput sequencing offers high-resolution data regarding the microbial …
Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case
Background Chloroplasts are organelles that conduct photosynthesis in plant and algal
cells. The information chloroplast genome contained is widely used in agriculture and …
cells. The information chloroplast genome contained is widely used in agriculture and …
Benchmarking long-read assemblers for genomic analyses of bacterial pathogens using oxford nanopore sequencing
Oxford Nanopore sequencing can be used to achieve complete bacterial genomes.
However, the error rates of Oxford Nanopore long reads are greater compared to Illumina …
However, the error rates of Oxford Nanopore long reads are greater compared to Illumina …
The impact of applying various de novo assembly and correction tools on the identification of genome characterization, drug resistance, and virulence factors of …
HA Safar, F Alatar, K Nasser, R Al-Ajmi, W Alfouzan… - BMC …, 2023 - Springer
Oxford Nanopore sequencing technology (ONT) is currently widely used due to its
affordability, simplicity, and reliability. Despite the advantage ONT has over next-generation …
affordability, simplicity, and reliability. Despite the advantage ONT has over next-generation …
Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively …
B Bogaerts, S Nouws, B Verhaegen… - Microbial …, 2021 - microbiologyresearch.org
Whole genome sequencing (WGS) enables complete characterization of bacterial
pathogenic isolates at single nucleotide resolution, making it the ultimate tool for routine …
pathogenic isolates at single nucleotide resolution, making it the ultimate tool for routine …
Benchmarking of computational error-correction methods for next-generation sequencing data
Background Recent advancements in next-generation sequencing have rapidly improved
our ability to study genomic material at an unprecedented scale. Despite substantial …
our ability to study genomic material at an unprecedented scale. Despite substantial …