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 and has only one block.

       -r <string>
              Name  of  an  input  read  file. Acceptable formats include gzipped FASTQ and FASTQ (automatically
              identified).

       -o <string>
              Name of an output file in BAM format.

       ## Optional arguments: # input reads and output

       --SAMoutput
              Save mapping results in SAM format.

       # number of CPU threads

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

       # others

       -v     Output version of the program.

       -X     Turn on the RNA-seq mode.

       Refer to Users Manual for detailed description to the arguments.

sublong 2.0.0+dfsg                               September 2019                                       SUBLONG(1)