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

Fritz J Sedlazeck; Hayan Lee; Charlotte A Darby; Michael C Schatz

doi:10.1038/s41576-018-0003-4

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

Nat Rev Genet. 2018 Jun;19(6):329-346. doi: 10.1038/s41576-018-0003-4.

Authors

Fritz J Sedlazeck¹, Hayan Lee², Charlotte A Darby³, Michael C Schatz^{4

5}

Affiliations

¹ Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
² Department of Genetics, Stanford University, Stanford, CA, USA.
³ Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
⁴ Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. [email protected].
⁵ Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. [email protected].

PMID: 29599501
DOI: 10.1038/s41576-018-0003-4

Abstract

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 before. These long-range technologies are rapidly advancing the field with improved reference genomes, more comprehensive variant identification and more complete views of transcriptomes and epigenomes. However, they also require new bioinformatics approaches to take full advantage of their unique characteristics while overcoming their complex errors and modalities. Here, we discuss several of the most important applications of the new technologies, focusing on both the currently available bioinformatics tools and opportunities for future research.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Review

MeSH terms

Animals
Chromosome Mapping / methods*
Computational Biology / methods*
Gene Expression Profiling / methods*
Genomics / methods*
High-Throughput Nucleotide Sequencing / methods*
Humans
Transcriptome*