Opportunities and challenges in long-read sequencing data analysis
Top Cited Papers
Open Access
- 7 February 2020
- journal article
- review article
- Published by Springer Science and Business Media LLC in Genome Biology
- Vol. 21 (1), 1-16
- https://doi.org/10.1186/s13059-020-1935-5
Abstract
Long-read technologies are overcoming early limitations in accuracy and throughput, broadening their application domains in genomics. Dedicated analysis tools that take into account the characteristics of long-read data are thus required, but the fast pace of development of such tools can be overwhelming. To assist in the design and analysis of long-read sequencing projects, we review the current landscape of available tools and present an online interactive database, long-read-tools.org, to facilitate their browsing. We further focus on the principles of error correction, base modification detection, and long-read transcriptomics analysis and highlight the challenges that remain.Keywords
This publication has 150 references indexed in Scilit:
- Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcriptionJournal of Nanobiotechnology, 2013
- Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop CodonsCell, 2012
- Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variationNucleic Acids Research, 2012
- The importance of identifying alternative splicing in vertebrate genome annotationDatabase: The Journal of Biological Databases and Curation, 2012
- The Origins, Evolution, and Functional Potential of Alternative Splicing in VertebratesMolecular Biology and Evolution, 2011
- Mapping copy number variation by population-scale genome sequencingNature, 2011
- Direct detection of DNA methylation during single-molecule, real-time sequencingNature Methods, 2010
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression dataBioinformatics, 2009
- Alternative isoform regulation in human tissue transcriptomesNature, 2008
- Accurate whole human genome sequencing using reversible terminator chemistryNature, 2008