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"
https://academic.oup.com/gigascience/article/9/5/giaa046/5835778
- The main script is pipeline.sh
- Results from pipeline can be visualize with the python notebook exploring.ipynb
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