NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes. - Gabriel A. Al-Ghalith; Emmanuel Montassier; Henry N. Ward; Dan Knight (PLoS Comput. Biol., 2016)

SHOGUN: a modular, accurate and scalable framework for microbiome quantification. - Benjamin Hillmann; Gabriel A. Al-Ghalith; Robin R. Shields-Cutler; Qiyun Zhu; Rob Knight 001; Dan Knight (Bioinform., 2020)