NAME

       sublong - toolkit for processing next-gen sequencing data

DESCRIPTION

       Please specify the input, output files and the index.

       Sublong v2.0.1

       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.

AUTHOR

        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.