Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data.
Nat Commun
; 13(1): 1321, 2022 03 14.
Article
in English
| MEDLINE | ID: covidwho-1740438
ABSTRACT
Infectious disease monitoring on Oxford Nanopore Technologies (ONT) platforms offers rapid turnaround times and low cost. Tracking low frequency intra-host variants provides important insights with respect to elucidating within-host viral population dynamics and transmission. However, given the higher error rate of ONT, accurate identification of intra-host variants with low allele frequencies remains an open challenge with no viable computational solutions available. In response to this need, we present Variabel, a novel approach and first method designed for rescuing low frequency intra-host variants from ONT data alone. We evaluate Variabel on both synthetic data (SARS-CoV-2) and patient derived datasets (Ebola virus, norovirus, SARS-CoV-2); our results show that Variabel can accurately identify low frequency variants below 0.5 allele frequency, outperforming existing state-of-the-art ONT variant callers for this task. Variabel is open-source and available for download at www.gitlab.com/treangenlab/variabel .
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Nanopores
/
Nanopore Sequencing
/
COVID-19
Type of study:
Experimental Studies
Topics:
Variants
Limits:
Humans
Language:
English
Journal:
Nat Commun
Journal subject:
Biology
/
Science
Year:
2022
Document Type:
Article
Affiliation country:
S41467-022-28852-1
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