IVAR(1)

✨ IVAR(1) ✨

okay bestie, gather round, because this is the ivar manual page and it's literally the moment 💅 it lives in the User Commands section of the manual, so if you were looking for some dusty old system utility... no ma'am, this is the viral sequencing one 🦋

🌸 NAME 🌸

ivar — functions broadly useful for viral amplicon-based sequencing

🎀 SYNOPSIS 🎀

ivar [command
<trim|variants|filtervariants|consensus|getmasked|removereads|version|help>]

💖 DESCRIPTION 💖

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. bestie, it's giving toolbox energy 🧰✨

Additional tools for metagenomic sequencing are actively being incorporated into iVar — so it's a work in progress and that's iconic of it, honestly.

so here's the tea: 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. like, yes, you could Frankenstein it together yourself, but why would you when iVar already ate 🔥

👑 COMMANS 👑

(no I did not make a typo, that's what the original says, and honestly? main character energy of it 🙈)

• trim — trim reads in aligned BAM file
• variants — call variants from aligned BAM file
• filtervariants — filter variants across replicates or samples
• consensus — call consensus from aligned BAM file
• getmasked — detect primer mismatches and get primer indices for the amplicon to be masked
• removereads — remove reads from trimmed BAM file
• version — show version information

💡 to view detailed usage for each command type, run:

ivar <command>

and yes, bestie, help is in the synopsis too, so if you're lost just go poke at it 🫶

💜 AUTHOR 💜

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. no cap, we love a documented manpage 💖

🌈 see ya 🌈

and that's the whole thing!! this page is from ivar 1.2.2, dated May 2020, living its best life in section 1 of the manual (you know, the User Commands girlies). go call some variants, bestie, you got this 💅✨🦋