bwa shm looks very interesting, especially if you have a smallish cluster for your own use.
But unfortunately there is almost no documentation.
What I know:
- you can do "
bwa shm <indexfile>" and it will load the index into RAM. This means it will create /dev/shm/bwactl and /dev/shm/bwaidx-<indexfile>.
bwa shm -ddeletes the files in /dev/shm, bwa shm -l lists them
- all subsequent invocations of "
bwa mem" will be almost instant.
- for this to work, use the full pathname with bwa shm, e.g.
bwa shm /my/data/dir/hg19.fa
- for the subsequent run of bwa mem, use just the basename, e.g.
bwa mem hg19.fa
- I can't get
bwa alnto work with this, apparently it doesn't support the pre-loaded index (yet?)
bwaswalso does not seem to support a pre-loaded index
Is there a way to get aln or samse support?
Does any other operation support the pre-loaded index?