sublong - toolkit for processing next-gen sequencing data

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

sublong 2.0.3                                      March 2023                                         SUBLONG(1)

       Please specify the input, output files and the index.

       Sublong v2.0.4

       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 - toolkit for processing next-gen sequencing data