Documentation {#mainpage}
============

* [Installation](@ref installpage)
* [Manual](@ref manualpage)
* [Cookbook](@ref cookbookpage)

Publication
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[An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar](https://doi.org/10.1186/s13059-018-1618-7)

*Genome Biology* 2019 **20**:8

Nathan D Grubaugh, Karthik Gangavarapu, Joshua Quick, Nathaniel L Matteson, Jaqueline Goes De Jesus, Bradley J Main, Amanda L Tan, Lauren M Paul, Doug E Brackney, Saran Grewal, Nikos Gurfield, Koen KA Van Rompay, Sharon Isern, Scott F Michael, Lark L Coffey, Nicholas J Loman, Kristian G Andersen

bioRxiv doi: [https://doi.org/10.1101/383513](https://doi.org/10.1101/383513)
