Virus Detection

The Following example shows how to perform virus detection analysis. For up- and down-stream relationship, please see “Up Down Stream Flowchart” part.

virus detection Example usage

from cfDNApipe import *
import glob

pipeConfigure(
   threads=60,
   genome="hg19",
   refdir=r"path_to_reference/hg19",
   outdir=r"path_to_output/virus_output",
   data="WGS",
   type="paired",
   build=True,
   JavaMem="10g",
)

# Download and Build Virus Genome
Configure.virusGenomeCheck(folder="path_to_reference/virus_database", build=True)

# paired data
fq1 = glob.glob("path_to_unmapped/*.fq.1.gz")
fq2 = glob.glob("path_to_unmapped/*.fq.2.gz")

virusdetect(seqInput1=fq1, seqInput2=fq2, upstream=True)