References
Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, et al.: TheSorcerer IIGlobal Ocean Sampling expedition: expanding the universe of protein families.PLoS Biol 2007, 5:e16.
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, et al.: A human gut microbial gene catalogue established by metagenomic sequencing.Nature 2010, 464:59–65.
Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI: The Human Microbiome Project.Nature 2007, 449:804–810.
Brady A, Salzberg SL: Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models.Nat Methods 2009, 6:673–676.
McHardy AC, Martin HG, Tsirigos A, Hugenholtz P, Rigoutsos I: Accurate phylogenetic classification of variable-length DNA fragments.Nat Methods 2007, 4:63–72.
Nalbantoglu OU, Way SF, Hinrichs SH, Sayood K: RAIphy: phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles.BMC Bioinformatics 2011, 12:41.
Patil KR, Haider P, Pope PB, Turnbaugh PJ, Morrison M, Scheffer T, McHardy AC: Taxonomic metagenome sequence assignment with structured output models.Nat Methods 2011, 8:191–192.
Laserson J, Jojic V, Koller D: Genovo: de novo assembly for metagenomes.J Comput Biol 2011, 18:429–443.
Peng Y, Leung HC, Yiu SM, Chin FY: Meta-IDBA: ade novoassembler for metagenomic data.Bioinformatics 2011, 27:i94-i101.
MetAMOS Source Code [https://github.com/treangen/metAMOS]
Li Y, Hu Y, Bolund L, Wang J: State of the artde novoassembly of human genomes from massively parallel sequencing data.Hum Genomics 2010, 4:271–277.
Sommer DD, Delcher AL, Salzberg SL, Pop M: Minimus: a fast, lightweight genome assembler.BMC Bioinformatics 2007, 8:64.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Treangen, T.J., Koren, S., Astrovskaya, I. et al. MetAMOS: a metagenomic assembly and analysis pipeline for AMOS. Genome Biol 12 (Suppl 1), P25 (2011). https://doi.org/10.1186/1465-6906-12-S1-P25
Published:
DOI: https://doi.org/10.1186/1465-6906-12-S1-P25