4.14. jsa.np.rtSpeciesTyping: Bacterial species typing with Oxford Nanopore sequencing

jsa.np.rtSpeciesTyping identify proportions of species from a DNA sample using Oxford Nanopore sequencing in real-time. It reads data in SAM/BAM format of the alignments of sequence reads to a collection of species genomes.

We provide a genome collection of nearly 1500 bacterial species on http://data.genomicsresearch.org/Projects/npAnalysis/. Refer to the documentation at https://github.com/mdcao/npAnalysis/ for more details.

4.14.1. Synopsis

jsa.np.rtSpeciesTyping: Realtime species typing using Nanopore Sequencing data

4.14.2. Usage

jsa.np.rtSpeciesTyping [options]

4.14.3. Options

--output=s Output file, - for standard output (default=’output.dat’)
--bamFile=s The bam file (REQUIRED)
--indexFile=s indexFile (REQUIRED)
--qual=d Minimum alignment quality (default=‘1.0’)
--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’)
--web Whether to use Web visualization. (default=’false’)
--log Whether to write mapping details to species2reads.map. (default=’false’)
--help Display this usage and exit (default=’false’)

4.14.5. Usage examples

If there is a sam/bam file of aligning the Nanopore sequencing to the genome collection, the program can read from this

jsa.np.rtSpeciesTyping -bam alignment.sam -index SpeciesTyping/Bacteria/speciesIndex --read 50 -time 60 -out speciesTypingResults.out

This program can read data from the output stream of an alignment program to perform analysis in real-time. For example, one can create such a pipeline to listen on port 3456

jsa.util.streamServer -port 3456 \
| bwa mem -t 10 -k11 -W20 -r10 -A1 -B1 -O1 -E1 -L0 -Y -K 10000 SpeciesTyping/Bacteria/genomeDB.fasta - 2> /dev/null \
| jsa.np.rtSpeciesTyping -bam - -index SpeciesTyping/Bacteria/speciesIndex --read 50 -time 60 -out speciesTypingResults.out 2>  speciesTypingResults.log &

and streams data to this pipeline using npReader:

jsa.np.npreader -GUI -realtime -folder <DownloadFolder> -fail -output data.fastq -stream serverAddress:3456