What are "Base-Space" reads? [BWA]

[dp05yk]

This is more of an efficiency question - the BWA 'sampe' command provides an option to 'pre-load' the index into memory. If this option is not selected, BWA has to reload the index into memory every 262144 reads. It seems inefficient, for instance if you had 262145 reads, you would reload the index just to map one more read.

I'm just wondering what 'base-space' reads are since it's only available for those (I'm assuming Illumina, as SOLiD reads are considered colour space?), and why this option wouldn't be a default since it really seems to be much more efficient?

Also, if someone somehow knows this, I'm wondering why this option wouldn't be available for colour space reads.

[ECO]

Moving to Bioinformatics to get other opinions, and the answer to your BWA question.

"Basespace" refers to SOLiD reads that have been converted from "colorspace", usually by mapping to the reference.

One (bad) way to do this is to directly convert colorspace into the bases implied by the color calls. This is bad because any single color error borks the rest of the read.

It may or may not also refer to "double-encoded" SOLiD reads (which is the old terrible idea of converting colorspace reads to an ACGT string that can be handled by mapping programs). I don't think anyone still does this as there are several colorspace competent mapping programs. We used to call this "fakebase".

[odoyle81]

Kind of surprised there have been no replies?
Does anyone use the -P option of bwa sampe with illumina reads?
When it says "With this option, at least 1.25N bytes of memory are required, where N is the length of the genome." are the units of the length of the genome in bp?
so expected memory needed for 400mb genome is 400mb x 1.25 = 500mb?

[nilshomer]

Your right, base space reads are those that produce bases (454, Illumina, etc.).

As for why is "-P" not on by default, I believe that with human the index with this option on would make the memory required over 8GB, which was a crucial limit a few years ago (we all have 128GB now right?).