Fig. 1

Overview of a read alignment algorithm. a The seeds from the reference genome sequence are extracted. b Each extracted seed and all its occurrence locations in the reference genome are stored using the data structure of choice (suffix tree and hash table are presented as an example). Common prefixes of the seeds are stored once in the branches of the suffix tree, while the hash table stores each seed individually. c The seeds from each read sequence are extracted. d The occurrences of each extracted seed in the reference genome are determined by querying the index database. In this example, the three seeds from the first read appear adjacent at locations 5, 7, and 9 in the reference genome. Two of the same seeds appear also adjacent at another two locations (12 and 16). Other non-adjacent locations are filtered out (marked with X) as they may not span a good match with the first read. e The adjacent seeds are linked together to form a longer chain of seeds by examining the mismatches between the gaps. Pre-alignment filters can also be applied to quickly decide whether or not the computationally expensive DP calculation is needed. f Once the pre-alignment filter accepts the alignment between a read and a region in the reference genome, then DP-based (or non-DP-based) verification algorithms are used to generate the alignment file (in BAM or SAM formats), which contains alignment information such as the exact number of differences, location of each difference, and their type.