Opportunities and challenges in long-read sequencing data analysis

By Shanika L. Amarasinghe, Shian Su, Xueyi Dong, Luke Zappia, Matthew E. Ritchie, Quentin Gouil. Genome Biology, 2020

1,305 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/63ca65b938c64667c17e74ff0a9003925ff02ce8

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In Molecular Biology

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Citations in the corpus

• hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data (2023, background): “6 Cell Reports Methods 3, 100498, June 26, 2023 assays capture information at the gene level, thereby missing much of the biological diversity and regulatory mechanisms that occurs at the isoform level.(30) Emerging long-read sequencing approaches enable us to profile cellular transcriptomes at isof”
• YaHS: yet another Hi-C scaffolding tool (2022, neutral): “Despite the technological advances, the assembly of reference-quality genomes with long-read sequencing data alone remains elusive (Amarasinghe et al. , 2020).”
• Nanopore sequencing technology, bioinformatics and applications (2021, methodology): “Compared to PacBio, ONT performs better in detecting 5mC but has lower accuracy in detecting 6mA 68,75,81 .”
• DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing (2023, neutral): “Oxford Nanopore Technologies (ONT), can directly sequence native DNA without PCR ampli fi cation 12,13 .”