An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
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PROVIDER: PRJEB30574 | ENA |
REPOSITORIES: ENA
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Project description:How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentration, sequencing coverage, primer mismatches, and replicates influence the accuracy of measuring intrahost virus diversity. We develop an experimental protocol and computational tool, iVar, for using PrimalSeq to measure virus diversity using Illumina and compare the results to Oxford Nanopore sequencing. We demonstrate the utility of PrimalSeq by measuring Zika and West Nile virus diversity from varied sample types and show that the accumulation of genetic diversity is influenced by experimental and biological systems.
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Project description:We aimed to create an ovary cell atlas using publicly available RNA-seq data. To complement the data we sequenced 2 ovary tissue samples from patients undergoing elective surgery at the JR hospital in Oxford. We applied single-nucei sequencing using the 10x Chromium technology.
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