Genopo: a nanopore sequencing analysis toolkit for portable Android devices.
Betacoronavirus
/ genetics
COVID-19
Cell Phone
/ instrumentation
Computational Biology
/ instrumentation
Coronavirus Infections
/ diagnosis
DNA Methylation
Genome, Human
Genome, Viral
High-Throughput Nucleotide Sequencing
/ instrumentation
Humans
Nanopores
Pandemics
Pneumonia, Viral
/ diagnosis
SARS-CoV-2
Whole Genome Sequencing
/ instrumentation
Journal
Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179
Informations de publication
Date de publication:
29 09 2020
29 09 2020
Historique:
received:
08
06
2020
accepted:
04
09
2020
entrez:
30
9
2020
pubmed:
1
10
2020
medline:
21
10
2020
Statut:
epublish
Résumé
The advent of portable nanopore sequencing devices has enabled DNA and RNA sequencing to be performed in the field or the clinic. However, advances in in situ genomics require parallel development of portable, offline solutions for the computational analysis of sequencing data. Here we introduce Genopo, a mobile toolkit for nanopore sequencing analysis. Genopo compacts popular bioinformatics tools to an Android application, enabling fully portable computation. To demonstrate its utility for in situ genome analysis, we use Genopo to determine the complete genome sequence of the human coronavirus SARS-CoV-2 in nine patient isolates sequenced on a nanopore device, with Genopo executing this workflow in less than 30 min per sample on a range of popular smartphones. We further show how Genopo can be used to profile DNA methylation in a human genome sample, illustrating a flexible, efficient architecture that is suitable to run many popular bioinformatics tools and accommodate small or large genomes. As the first ever smartphone application for nanopore sequencing analysis, Genopo enables the genomics community to harness this cheap, ubiquitous computational resource.
Identifiants
pubmed: 32994472
doi: 10.1038/s42003-020-01270-z
pii: 10.1038/s42003-020-01270-z
pmc: PMC7524736
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
538Subventions
Organisme : Cancer Institute NSW (Cancer Institute New South Wales)
ID : 2018/ECF013
Pays : International
Organisme : Department of Health | National Health and Medical Research Council (NHMRC)
ID : APP1173594
Pays : International
Références
Jain, M., Olsen, H. E., Paten, B. & Akeson, M. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol. 17, 239 (2016).
doi: 10.1186/s13059-016-1103-0
Quick, J. et al. Real-time, portable genome sequencing for Ebola surveillance. Nature 530, 228–232 (2016).
doi: 10.1038/nature16996
Goordial, J. et al. In situ field sequencing and life detection in remote (79°26’N) Canadian High arctic permafrost ice wedge microbial communities. Front. Microbiol. 8, 2594 (2017).
doi: 10.3389/fmicb.2017.02594
Castro-Wallace, S. L. et al. Nanopore DNA sequencing and genome assembly on the international space station. Sci. Rep. 7, 18022 (2017).
doi: 10.1038/s41598-017-18364-0
Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
doi: 10.1093/bioinformatics/bty191
Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987–2993 (2011).
doi: 10.1093/bioinformatics/btr509
Simpson, J. T. et al. Detecting DNA cytosine methylation using nanopore sequencing. Nat. Methods 14, 407–410 (2017).
doi: 10.1038/nmeth.4184
Gamaarachchi, H. et al. GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis. BMC Bioinformatics 21, 343 (2020).
doi: 10.1186/s12859-020-03697-x
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
doi: 10.1093/bioinformatics/btq033
Gamaarachchi, H., Parameswaran, S. & Smith, M. A. Featherweight long read alignment using partitioned reference indexes. Sci. Rep. 9, 4318 (2019).
doi: 10.1038/s41598-019-40739-8
Jain, M. et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat. Biotechnol. 36, 338–345 (2018).
doi: 10.1038/nbt.4060
Quick, J. et al. Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol. 16, 114 (2015).
doi: 10.1186/s13059-015-0677-2
Quick, J. et al. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat. Protoc. 12, 1261–1276 (2017).
doi: 10.1038/nprot.2017.066
Eden, J.-S. et al. An emergent clade of SARS-CoV-2 linked to returned travellers from Iran. Virus Evol. 6, veaa027 (2020).