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’)
4.14.4. See also¶
jsa.np.npreader, jsa.np.rtStrainTyping, jsa.np.rtResistGenes, jsa.util.streamServer, jsa.util.streamClient
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