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Fig. 4 | BMC Bioinformatics

Fig. 4

From: An efficient error correction algorithm using FM-index

Fig. 4

Illustration of heuristic alignment using common SA intervals during FM-index extension. a The SA intervals of all k-mers (k=3) in query are pre-computed and stored in an array A[i]. The forward-extended base (T) has an SA interval [10,22] inclusive within the interval [10,25] in A[i], which implies that the query and the compressed reads share common k-mer (GAT) at this locus; b Mismatches and indels will temporarily lead to no common k-mers (i.e., SA intervals in FM-index) found. In order to tolerate indels, the SA interval of any newly-extended base must be compared with those in a range according to the maximum indels allowed

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