bwtsw algorithm in bwa

[javijevi]

Hi, all,

I want to check bwa to align 25 bp SOLiD reads to a 800 MB reference genome, and have a question about the -a parameter ("algorithm for constructing BWT index") in the 'bwa index' step.

Since I'm not going to use the 'bwa dbwtsw' algorithm for the alignment step (which is only recommended for longer reads), do I must use the default '-a is' option for the 'bwa index' step?

Or, on the contrary, the '-a bwtsw' parameter in the index creation step and the 'bwa dbwtsw' algorithm in the alignment step are absolutely independent one each other, and their similar names are casual, so that I can use the '-a bwtsw' option irrespectively of the algorithm used in the alignment step?

I cannot see it clearly from the documentation.

Thanks in advance.

[lh3]

For 800Mbp genome, use "-a bwtsw". Using "-a is" is also fine, but it may take >4GB memory.

[javijevi]

For 800Mbp genome, use "-a bwtsw". Using "-a is" is also fine, but it may take >4GB memory.

I can use a machine with 32 GB RAM, so this will not be a problem. Do you still recommend to use '-a btwsw', even if I'm not going to use 'bwa dbwtsw' in the alignment step?