BWA: reference sequences longer than 4GB

[ElMichael]

Hi,
I have many reference sequences that in total exceed 4GB. Is there any way to use BWA alignment against all these sequences simultaneously? Or I have to split a fasta file on two files, generate two databases, and align data separately (that doesn't work for me)?

[sklages]

The FAQ of bwa is pretty clear in this point,

Does BWA work on reference sequences longer than 4GB in total?
No, this is not possible and will not be supported in the near future due to
 the technical complexity involved.

Though I never had such a large reference, I assume you have to split your reference.