the text can be up to 5M characters

No matter how you generate them, just storing the 5 million rotations of 5 million characters (>23 Terabytes of data) is going to be a problem, long before you get to the point of trying to sort.

If the purpose of your BWT generation is to aid compression, then there are much more effective and efficient methods of compressing genomic data.

If the purpose is Short Read Alignment, you almost certainly need to look at the suffix trie methods described there.

With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'
Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
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In reply to Re^3: Is it possible to make reference to substrings and sort them? by BrowserUk
in thread Is it possible to make reference to substrings and sort them? by spooknick

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