From: Technology dictates algorithms: recent developments in read alignment
Hashing | Suffix tree and BWT-FM | |
---|---|---|
Easy to implement | Yes | No |
Search for exact/inexact match | Exact | Exact and inexact |
Index size | Large | Compressed (small) |
Indexing time | Small | Large |
Seed query speed | O(1), fast | Slow |
Seed length | Fixed length per index | Can be fixed or variable |