Bibliography

Altschul et al., 1990

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990).
Basic local alignment search tool.
Journal of molecular biology, 215(3):403-410.

Hughes et al., 2002

Hughes, J. B., Hellmann, J. J., Ricketts, T. H., and Bohannan, B. J. (2002).
Counting the uncountable: Statistical approaches to estimating microbial diversity.
Applied and environmental microbiology, 68(1):448.

Langmead and Salzberg, 2012

Langmead, B. and Salzberg, S. L. (2012).
Fast gapped-read alignment with Bowtie 2.
Nature Methods, 9(4):357-359.

Linke et al., 2011

Linke, B., Giegerich, R., and Goesmann, A. (2011).
Conveyor: a workflow engine for bioinformatic analyses.
Bioinformatics, 27(7):903-911.

Liu et al., 2012

Liu, J., Wang, H., Yang, H., Zhang, Y., Wang, J., Zhao, F., and Qi, J. (2012).
Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms.
Nucleic Acids Research, page gks828.

Mavromatis et al., 2007

Mavromatis, K., Ivanova, N., Barry, K., Shapiro, H., Goltsman, E., McHardy, A. C., Rigoutsos, I., Salamov, A., Korzeniewski, F., Land, M., et al. (2007).
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods.
Nature Methods, 4(6):495-500.

Niu et al., 2011

Niu, B., Zhu, Z., Fu, L., Wu, S., and Li, W. (2011).
FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes.
Bioinformatics, 27(12):1704-1705.

Simpson, 1949

Simpson, E. H. (1949).
Measurement of diversity.
Nature.

Spellerberg and Fedor, 2003

Spellerberg, I. F. and Fedor, P. J. (2003).
A tribute to Claude Shannon (1916-2001) and a plea for more rigorous use of species richness, species diversity and the Shannon-Wiener Index.
Global ecology and biogeography, 12(3):177-179.

Wood and Salzberg, 2014

Wood, D. and Salzberg, S. (2014).
Kraken: ultrafast metagenomic sequence classification using exact alignments.
Genome Biol, 15(3):R46.