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’)

4.15.5. Setting up

Refer to real-time analysis page at https://github.com/mdcao/npAnalysis/