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