NAME

       subread-buildindex - toolkit for processing next-gen sequencing data

DESCRIPTION

       Version 2.0.1

       Usage:

              ./subread-buildindex [options] -o <basename> {FASTA[.gz] file1}\

              [FASTA[.gz] file2] ...

       Required arguments:

       -o <basename>
              base name of the index to be created

       Optional arguments:

       -F     build  a  full index for the reference genome. 16bp subreads will be extracted from
              every position of the reference genome. Size of the index is typically 3 times  the
              size of index built from using the default setting.

       -B     create  one block of index. The built index will not be split into multiple pieces.
              This makes the largest amount of memory be requested when running  alignments,  but
              it  enables the maximum mapping speed to be achieved. This option overrides -M when
              it is provided as well.

       -M <int>
              size of requested memory(RAM) in megabytes, 8000 by default.

       -f <int>
              specify the threshold for removing uninformative subreads (highly repetitive 16mers
              in the reference). 100 by default.

       -c     build a color-space index.

       -v     output version of the program.

       For more information about these arguments, please refer to the User Manual.

AUTHOR

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