iVar: Cookbook
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

Cookbook

Two pipelines to call iSNVs from known and unknown reference sequences have been written in snakemake.

The two pipelines are distributed along with iVar and are present in thepipeline/ and pipeline_field/ fodlers respectively.

For both pipelines, there are four parameters that will have to be set in beginning of the Snakefile.

in_dir = "<input fastq files>"
out_dir = "<output directory>"
bed = "<bed-file-with-primer-positions>"
ref="<path to reference fasta>"

### Call iSNVs from samples with known reference sequence

Link to Jupyter Notebook

Link to pipeline

#### Dependencies:

- iVar
- samtools
- bwa
- bedtools

### Call iSNVs from samples with unknown reference sequence

Link to pipeline

#### Dependencies:

- iVar
- samtools
- bwa
- bedtools