4.17. jsa.np.rtResistGenes: Antibiotic resistance gene identification in real-time with Nanopore sequencing

jsa.np.rtResistGenes identifies antibiotic resistance genes from real-time sequencing with Nanopore MinION.

4.17.1. Synopsis

jsa.np.rtResistGenes: Realtime identification of antibiotic resistance genes from Nanopore sequencing

4.17.2. Usage

jsa.np.rtResistGenes [options]

4.17.3. Options

--output=s Output file (default=’output.dat’)
--bamFile=s The bam file (default=’null’)
--score=d The alignment score threshold (default=‘1.0E-4’)
--msa=s Name of the msa method, support poa, kalign, muscle and clustalo (default=’kalign’)
--tmp=s Temporary folder (default=’_tmpt’)
--resDB=s Path to resistance database (REQUIRED)
--qual=d Minimum alignment quality (default=‘0.0’)
--twodonly Use only two dimentional reads (default=’false’)
--read=i Minimum number of reads between analyses (default=‘50’)
--time=i Minimum number of seconds between analyses (default=‘1800’)
--thread=i Number of threads to run (default=‘4’)
--help Display this usage and exit (default=’false’)

4.17.5. Setting up

Refer to the documentation at https://github.com/mdcao/npAnalysis/ for more details.