iVar: Documentation
Author: Andersen Lab, The Scripps Research Institute
Description: iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar. While each of these functions can be accomplished using existing tools, iVar contains an intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates. We implemented the following functions in iVar: (1) trimming of primers and low-quality bases, (2) consensus calling, (3) variant calling - both iSNVs and insertions/deletions, and (4) identifying mismatches to primer sequences and excluding the corresponding reads from alignment files.
Keywords: variants calling,consensus,htslib,primal,primer,trimming,amplicon sequencing,ivar

iVar

Documentation

- Installation
- Manual
- Cookbook

# Publication

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

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