cookbookpage(3)

NAME
cookbookpage - 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