Comparison of the search accuracy of different alignment tools. (A) Taxonomic assignment of the query sequences in the simulated metagenomic analysis test was performed in the following steps: 1: Query sequences were generated by randomly selecting short fragments from reference genome sequences. 2: Sequence similarities were calculated between the query and reference genome sequences. 3: If a query matched to the original reference sequence, it was deleted from the results. 4: The best non-self hits were selected for taxonomic assignment. (B) Whether the result of taxonomic assignment were correct or not were assessed based on the taxonomic databases.