Rapid genotyping of targeted viral samples using Illumina short-read sequencing data.
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ABSTRACT:
SUBMITTER: Varadi A
PROVIDER: S-EPMC9481040 | biostudies-literature | 2022
REPOSITORIES: biostudies-literature
Publications
Rapid genotyping of targeted viral samples using Illumina short-read sequencing data.
Váradi Alex A Kaszab Eszter E Kardos Gábor G Prépost Eszter E Szarka Krisztina K Laczkó Levente L
PloS one 20220916 9
The most important information about microorganisms might be their accurate genome sequence. Using current Next Generation Sequencing methods, sequencing data can be generated at an unprecedented pace. However, we still lack tools for the automated and accurate reference-based genotyping of viral sequencing reads. This paper presents our pipeline designed to reconstruct the dominant consensus genome of viral samples and analyze their within-host variability. We benchmarked our approach on numero ...[more]
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