NAME

       subread-buildindex  -  builds  an  base-space  or  color-space  index  using the reference
       sequences

USAGE

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

       subread- 1.5.0-p1+dfsg-2