NAME

       sublong - long-read aligner that is designed based on seed-and-vote

USAGE

       sublong [options] -i <index_name> -r <input> -o <output>

       ## Mandatory arguments:

       -i <string>
              Base name of the index. The index must be built as a full index.

       -r <string>
              Name  of  an  input  read file. Acceptable formats include gzipped FASTQ, FASTQ and
              FASTA (automatically identified). The quality scores should  be  in  the  Phred  33
              format for the FASTQ or gzipped FASTQ formats.

       -o <string>
              Name of an output file. By default, the output is in BAM format.

       ## Optional arguments: # input reads and output

       --SAMoutput
              Save mapping results in SAM format.

       # thresholds for mapping

       -n <int>
              Number of selected subreads in a readlet, 85 by default.

       -m <int>
              Consensus threshold for mapping a readlet. 1 by default.

       -X <int>
              Maximum number of mis-matched bases allowed in each subread.  0 by default.

       # number of CPU threads

       -T <int>
              Number of CPU threads used. 1 by default.

       # others

       -v     Output version of the program.

       Refer to Users Manual for detailed description to the arguments.