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.TH "cookbookpage" 3 "iVar" \" -*- nroff -*-
.ad l
.nh
.SH NAME
cookbookpage \- Cookbook
.PP
.PP
Two pipelines to call iSNVs from known and unknown reference sequences have been written in \fRsnakemake\fP\&.
.PP
The two pipelines are distributed along with iVar and are present in the\fRpipeline/\fP and \fRpipeline_field/\fP fodlers respectively\&.
.PP
For both pipelines, there are four parameters that will have to be set in beginning of the Snakefile\&.
.PP
.PP
.nf
in_dir = "<input fastq files>"
out_dir = "<output directory>"
bed = "<bed\-file\-with\-primer\-positions>"
ref="<path to reference fasta>"
.fi
.PP
.PP
.PP
.SS "Call iSNVs from samples with known reference sequence"
.PP
\fRLink to Jupyter Notebook\fP
.PP
\fRLink to pipeline\fP
.PP
.SS "Dependencies:"
.PP
.IP "\(bu" 2
\fRiVar\fP
.IP "\(bu" 2
\fRsamtools\fP
.IP "\(bu" 2
\fRbwa\fP
.IP "\(bu" 2
\fRbedtools\fP
.PP
.PP
.SS "Call iSNVs from samples with unknown reference sequence"
.PP
\fRLink to pipeline\fP
.PP
.SS "Dependencies:"
.PP
.IP "\(bu" 2
\fRiVar\fP
.IP "\(bu" 2
\fRsamtools\fP
.IP "\(bu" 2
\fRbwa\fP
.IP "\(bu" 2
\fRbedtools\fP
.PP
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