xenial (1) subread-buildindex.1.gz

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