README.md

##NAHLN_AMR Scripts For questions, please contact Jessica Hicks: jessica.a.hicks@usda.gov

amr_wrapper.py usage:

Paths:

Must include path to amr_wrapper.py in $PATH.
Must also include this path in $PYTHONPATH.

Within the directory containing amr_wrapper.py these other 9 files are included:

• abricate_wrapper.py
• amr_wrapper.py
• amrfinder_wrapper.py
• latex_reporter.py
• lookup_genome_size.json
• mlst_wrapper.py
• rmlst.py
• seqsero2_wrapper.py
• sequence_score.py

In addition to the above files the following Python files must be in $PYTHONPATH.

• vsnp_fastq_quality.py
• spades_assembly.py
• spades_stats_parse.py
• kraken2_run.py

##Dependencies:

• Spades https://github.com/ablab/spades
• Kraken https://ccb.jhu.edu/software/kraken2/
• Kraken database; local path should be added to the script or updated to a variable.
• SeqSero https://github.com/denglab/SeqSero2
• MLST https://github.com/tseemann/mlst
• Abricate https://github.com/tseemann/abricate
• AMRFinder Plus https://github.com/ncbi/amr
• BLAST
• Python 3.7 or later

Many of these are also available from package managers such as Anaconda.

Run:

See amr_wrapper.py for run options.

Basic usage:

amr_wrapper.py -r1 *_R1*fastq.gz -r2 *_R2*fastq.gz