Classification of reads. (A) The figure shows how the score for a candidate at the species level is calculated. Given a 100-bp read, both the read (forward) and its reverse complement from right to left are searched. Centrifuge first identifies a short exact match, then continues until reaching a mismatch: The first 40-bp segment exactly matches six species (A, B, C, D, E, F), followed by a mismatch at the 41st base; the second 26-bp segment matches two species (G and H), followed by a mismatch at the 68th base; and the third 32-bp segment matches only species G. This procedure is repeated for the reverse complement of the read. Centrifuge assigns the highest score (625) to species A, B, C, D, E, and F. (B) Centrifuge then traverses up the taxonomic tree to reduce the number of assignments, first by considering the genus that includes the largest number of species, genus I, which covers species A, B, and C, and then replacing these three species with the genus. This procedure results in reducing the number of assignments to four (genus I plus species D, E, and F).
