Ocean Resistome pipeline

This repository host the scripts used in the article "Global ocean resistome revealed: exploring Antibiotic Resistance Gene (ARGs) abundance and distribution on TARA oceans samples"

Pre-requisites

MetaGeneMark
DeepARG
PlasFlow
Kaiju
MicrobeCensus
BBMAP
NCBI-tools (fastq-dump)
samtools
seqkit
python3 (with libraries pandas, ete3, numpy)
Jupyter (for data exploring/visualization) and python libraries: matplotlib, seaborn, statsmodels, networkx and scipy

Name		Name	Last commit message	Last commit date
Latest commit History 24 Commits
scripts.RCuadrat		scripts.RCuadrat
LICENSE		LICENSE
README.md		README.md
contig_gene_id_table_generator.py		contig_gene_id_table_generator.py
deep_ARG.sh		deep_ARG.sh
exploring.ipynb		exploring.ipynb
faidx_extract.sh		faidx_extract.sh
fixing_header.sh		fixing_header.sh
generate_contig_infos.sh		generate_contig_infos.sh
get_contigs.sh		get_contigs.sh
get_data.sh		get_data.sh
get_fasta_phy.sh		get_fasta_phy.sh
get_reads.sh		get_reads.sh
parser_bbmap.py		parser_bbmap.py
parser_census.py		parser_census.py
parser_deepARG.py		parser_deepARG.py
parser_kaiju.py		parser_kaiju.py
parser_plasflow.py		parser_plasflow.py
pipeline.sh		pipeline.sh
run_bbmap.sh		run_bbmap.sh
run_kaiju.sh		run_kaiju.sh
run_metagenemark.sh		run_metagenemark.sh
run_microbe.sh		run_microbe.sh
run_plasFlow.sh		run_plasFlow.sh