| 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. |
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| Detect primer mismatches and get primer indices for the amplicon to be masked | 1.2.2+galaxy0 | 16.01 | |