Feature

• OneKey analysis from clean reads to variant VCF
• support multiple sample analysis
• parallel computing by default
• all analysis commands saved in files
• Servers with large memory recommended
• No QC procedure, using Clean reads as input

input file directory prepare

graph TB

analysisDir ---->fq
analysisDir-->sample.list.txt
fq-->*.R1.fq.gz
fq-->*.R2.fq.gz

analysisDir ---->genome
genome-->sequences.fa
genome-->genes.gtf

Dependencies

install dependencies using conda:

mamba create -n WGS perl=5.26.2 gatk4=4.2.5  bwa=0.7.17  samtools=1.15  vcftools=0.1.16 snpeff=5.1 python=3.7 parallel=20211222 bcftools=1.15 multiqc=1.12

Usage

#activate environment 
conda activate WGS

#change working directory to analysisDir
cd /mnt/d/workshop/3.ReSeq

#run
bash onekeyReseq

Results