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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