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)