Bioinformatics of nanopore sequencing

Makałowski, Wojciech; Shabardina, Victoria

doi:10.1038/s10038-019-0659-4

Cited by 32 publications

(23 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…In the future, one can expect new lncRNA annotation tools will be developed, such as new DNA and RNA sequencing methods (nanopore sequencing) and new bioinformatics methods [204,205]. The development of new methods of analysis, like mass spectroscopy makes it possible to detect biomolecules that bind to lncRNA, including proteins, peptides and low-molecular compounds.…”

Section: Concluding Remarks and Perspectivesmentioning

confidence: 99%

Human Long Noncoding RNA Interactome: Detection, Characterization and Function

Kazimierczyk

Kasprowicz

Kasprzyk

et al. 2020

IJMS

164

110

View full text Add to dashboard Cite

The application of a new generation of sequencing techniques has revealed that most of the genome has already been transcribed. However, only a small part of the genome codes proteins. The rest of the genome "dark matter” belongs to divergent groups of non-coding RNA (ncRNA), that is not translated into proteins. There are two groups of ncRNAs, which include small and long non-coding RNAs (sncRNA and lncRNA respectively). Over the last decade, there has been an increased interest in lncRNAs and their interaction with cellular components. In this review, we presented the newest information about the human lncRNA interactome. The term lncRNA interactome refers to cellular biomolecules, such as nucleic acids, proteins, and peptides that interact with lncRNA. The lncRNA interactome was characterized in the last decade, however, understanding what role the biomolecules associated with lncRNA play and the nature of these interactions will allow us to better understand lncRNA's biological functions in the cell. We also describe a set of methods currently used for the detection of lncRNA interactome components and the analysis of their interactions. We think that such a holistic and integrated analysis of the lncRNA interactome will help to better understand its potential role in the development of organisms and cancers.

show abstract

Section: Concluding Remarks and Perspectivesmentioning

confidence: 99%

Human Long Noncoding RNA Interactome: Detection, Characterization and Function

Kazimierczyk

Kasprowicz

Kasprzyk

et al. 2020

IJMS

164

110

View full text Add to dashboard Cite

show abstract

“…Since the first MinION release, the error rate has considerably improved thanks to changes in sequencing chemistry, the introduction of new base-calling algorithms, postsequencing correction tools and nanopore SNVs/insertions-deletions (INDELs) calling tools (Rang et al, 2018;Makałowski and Shabardina, 2019). Most of the substitution/deletion errors in nanopore reads occur in homopolymers, because their length is not correctly inferred from the electric signal (Rang et al, 2018).…”

Section: Target Gene Sequencingmentioning

confidence: 99%

“…Furthermore, error correction tools have already been tested (Minervini et al, 2016;Orsini et al, 2018;Makałowski and Shabardina, 2019); however, further improvements would be desirable to make the NS performance comparable to standard NGS technologies.…”

Section: Target Gene Sequencingmentioning

confidence: 99%

“…NS also allows the analysis of GC-rich regions or repeated regions that are difficult to study with conventional NGS sequencing approaches. As regards variant calling tools, starting from the methods used in the first works, many bioinformatic resources have been developed over time (Makałowski and Shabardina, 2019); moreover, in addition to custom procedures for phasing analysis, some specific software are currently available, such as the WhatsHap tool (Martin et al, 2016).…”

Section: Ns In Hematologymentioning

confidence: 99%

“…Regarding bioinformatics tools to be used for data analysis, dedicated pipelines/software have recently been developed and are currently available for nanopore RNA-seq analysis (Makałowski and Shabardina, 2019;Seki et al, 2019) (https:// long-read-tools.org/). Some applications are more efficiently performed with NS compared to short-read sequencing: the detection of fusion transcripts, the opportunity of identifying allele-specific transcriptional events by phasing variants on the transcripts, and single-cell transcriptome analysis (Seki et al, 2019).…”

Section: Transcriptome and Epitranscriptome Sequencingmentioning

confidence: 99%

See 2 more Smart Citations

Nanopore Sequencing in Blood Diseases: A Wide Range of Opportunities

et al. 2020

View full text Add to dashboard Cite

The molecular pathogenesis of hematological diseases is often driven by genetic and epigenetic alterations. Next-generation sequencing has considerably increased our genomic knowledge of these disorders becoming ever more widespread in clinical practice. In 2012 Oxford Nanopore Technologies (ONT) released the MinION, the first long-read nanopore-based sequencer, overcoming the main limits of short-reads sequences generation. In the last years, several nanopore sequencing approaches have been performed in various "-omic" sciences; this review focuses on the challenge to introduce ONT devices in the hematological field, showing advantages, disadvantages and future perspectives of this technology in the precision medicine era.

show abstract