This is the command subread-buildindex that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
Use subread-buildindex online using onworks.net services
