[HTML][HTML] Nanopore sequencing technology, bioinformatics and applications

Y Wang, Y Zhao, A Bollas, Y Wang, KF Au - Nature biotechnology, 2021 - nature.com
Rapid advances in nanopore technologies for sequencing single long DNA and RNA
molecules have led to substantial improvements in accuracy, read length and throughput …

Long-read human genome sequencing and its applications

GA Logsdon, MR Vollger, EE Eichler - Nature Reviews Genetics, 2020 - nature.com
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 …

Opportunities and challenges in long-read sequencing data analysis

SL Amarasinghe, S Su, X Dong, L Zappia, ME Ritchie… - Genome biology, 2020 - Springer
Long-read technologies are overcoming early limitations in accuracy and throughput,
broadening their application domains in genomics. Dedicated analysis tools that take into …

RNA sequencing: the teenage years

R Stark, M Grzelak, J Hadfield - Nature Reviews Genetics, 2019 - nature.com
Over the past decade, RNA sequencing (RNA-seq) has become an indispensable tool for
transcriptome-wide analysis of differential gene expression and differential splicing of …

Transcriptome assembly from long-read RNA-seq alignments with StringTie2

S Kovaka, AV Zimin, GM Pertea, R Razaghi… - Genome biology, 2019 - Springer
RNA sequencing using the latest single-molecule sequencing instruments produces reads
that are thousands of nucleotides long. The ability to assemble these long reads can greatly …

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

FJ Sedlazeck, H Lee, CA Darby, MC Schatz - Nature Reviews Genetics, 2018 - nature.com
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 …

Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue

SA Hardwick, W Hu, A Joglekar, L Fan, PG Collier… - Nature …, 2022 - nature.com
Single-nuclei RNA sequencing characterizes cell types at the gene level. However,
compared to single-cell approaches, many single-nuclei cDNAs are purely intronic, lack …

A survey of best practices for RNA-seq data analysis

A Conesa, P Madrigal, S Tarazona, D Gomez-Cabrero… - Genome biology, 2016 - Springer
Abstract RNA-sequencing (RNA-seq) has a wide variety of applications, but no single
analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data …

PacBio sequencing and its applications

A Rhoads, KF Au - Genomics, Proteomics and Bioinformatics, 2015 - academic.oup.com
Single-molecule, real-time sequencing developed by Pacific BioSciences offers longer read
lengths than the second-generation sequencing (SGS) technologies, making it well-suited …

RNA‐Seq methods for transcriptome analysis

R Hrdlickova, M Toloue, B Tian - Wiley Interdisciplinary …, 2017 - Wiley Online Library
Deep sequencing has been revolutionizing biology and medicine in recent years, providing
single base‐level precision for our understanding of nucleic acid sequences in high …