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’)

4.17.4. See also¶

jsa.np.npreader, jsa.np.rtSpeciesTyping, jsa.np.rtStrainTyping, jsa.util.streamServer, jsa.util.streamClient

4.17.5. Setting up¶

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