Overview of the CLAST search processing phases. (A) A read-only q-gram index was generated from reference genome sequences using a novel algorithm for parallel architecture (Figure 3). (B) The query sequences were searched against the read-only q-gram index. (C) Seeds were filtered to reduce calculation time (Figure 4). (D) The seed sequences were aligned to the reference genome sequences (Figure 2). (E) Results were filtered according to E-value and alignment length.