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 -d deletes 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 aln to work with this, apparently it doesn't support the pre-loaded index (yet?)
• bwasw also 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?