Using deepARG to detect Antibiotic Resistance Genes (ARGs)

#Using https://cge.food.dtu.dk/services/SCCmecFinder/ and http://genepi.food.dtu.dk/resfinder instead
#https://cge.food.dtu.dk/services/VirulenceFinder/

#https://github.com/gaarangoa/deeparg
#https://docs.conda.io/en/latest/miniconda.html

# -- install deepARG --
conda create -n deeparg_env python=2.7.18
source activate deeparg_env
mamba install -c bioconda diamond==0.9.24
mamba install -c bioconda trimmomatic
mamba install -c bioconda vsearch
mamba install -c bioconda bedtools==2.29.2
mamba install -c bioconda bowtie2==2.3.5.1
mamba install -c bioconda samtools

pip install git+https://github.com/gaarangoa/deeparg.git
deeparg download_data -o ~/Tools/deeparg/

conda activate deeparg_env

# -- run deeparg --
deeparg short_reads_pipeline --forward_pe_file ./raw_data/HDM1_R1.fastq.gz --reverse_pe_file ./raw_data/HDM1_R2.fastq.gz --output_file ./HDM1_arg_out -d ~/Tools/deeparg --bowtie_16s_identity 100
deeparg short_reads_pipeline --forward_pe_file ./raw_data/HDM7_R1.fastq.gz --reverse_pe_file ./raw_data/HDM7_R2.fastq.gz --output_file ./HDM7_arg_out -d ~/Tools/deeparg --bowtie_16s_identity 100
deeparg short_reads_pipeline --forward_pe_file ./raw_data/HDM10_R1.fastq.gz --reverse_pe_file ./raw_data/HDM10_R2.fastq.gz --output_file ./HDM10_arg_out -d ~/Tools/deeparg --bowtie_16s_identity 100
deeparg short_reads_pipeline --forward_pe_file ./raw_data/HDM11-SF1_R1.fastq.gz --reverse_pe_file ./raw_data/HDM11-SF1_R2.fastq.gz --output_file ./HDM11-SF1_arg_out -d ~/Tools/deeparg --bowtie_16s_identity 100
deeparg short_reads_pipeline --forward_pe_file ./raw_data/HDM15-SF2_R1.fastq.gz --reverse_pe_file ./raw_data/HDM15-SF2_R2.fastq.gz --output_file ./HDM15-SF2_arg_out -d ~/Tools/deeparg --bowtie_16s_identity 100

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