The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. - James R. Cole; Qiong Wang; E. Cardenas; Jordan A. Fish; Benli Chai; Ryan J. Farris; A. S. Kulam-Syed-Mohideen; Donna M. McGarrell; Terry L. Marsh; George M. Garrity; James M. Tiedje (Nucleic Acids Res., 2009)

Space-efficient read indexing and retrieval based on compressed de Bruijn graphs. - Meznah Almutairy; Jordan A. Fish; C. Titus Brown (ICCABS, 2013)

Ribosomal Database Project: data and tools for high throughput rRNA analysis. - James R. Cole; Qiong Wang; Jordan A. Fish; Benli Chai; Donna M. McGarrell; Yanni Sun; C. Titus Brown; Andrea Porras-Alfaro; Cheryl R. Kuske; James M. Tiedje (Nucleic Acids Res., 2014)

The khmer software package: enabling efficient nucleotide sequence analysis. - Michael R. Crusoe; Hussien F. Alameldin; Sherine Awad; Elmar Boucher; Adam Caldwell; Reed Cartwright; Amanda Charbonneau; Bede Constantinides; Greg Edvenson; Scott A. Fay; Jacob Fenton; Thomas Fenzl; et al. (F1000Research, 2015)