4.15. jsa.np.rtMLST: Multi-locus Sequencing Typing in real-time with Nanopore sequencing¶
jsa.np.rtMLST performs MLST typing from real-time sequencing with Nanopore MinION.
4.15.1. Synopsis¶
jsa.np.rtMLST: Realtime Multi-Locus Strain Typing using Nanopore Sequencing data
4.15.2. Usage¶
jsa.np.rtMLST [options]
4.15.3. Options¶
--output=s Output file (default=’output.dat’) --mlstScheme=s Path to mlst scheme (REQUIRED) --bamFile=s The bam file (default=’null’) --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=‘30’) --help Display this usage and exit (default=’false’)
4.15.4. See also¶
jsa.np.npreader, jsa.np.rtSpeciesTyping, jsa.np.rtStrainTyping, jsa.np.rtResistGenes, jsa.util.streamServer, jsa.util.streamClient
4.15.5. Setting up¶
Refer to real-time analysis page at https://github.com/mdcao/npAnalysis/