Also posted on biostars
bwa index -a bwtsw reference.fa
I got files. like .bwt file and .sa file. The naive way of generating these file is:
- Create all rotations of T
- Sort the rotations lexicographically
- Concatenate the last character of each rotation to form BWT(T)
I used this naive way in my algorithm. The problem is it took too much memory.
My question is: is there an effective memory way to generate .bwt file and .sa file ?
Any help will be appreciated.