Supported Programs

MetAMOS depends on many publically-available software tools. Below is a list of currently supported programs along with their citations:


EA-UTILS: Aronesty E. TOBioiJ : “Comparison of Sequencing Utility Programs”, DOI:10.2174/1875036201307010001, 2013.

PBcR: Koren S, Harhay GP, Smith TPL, Bono JL, Harhay DM, Mcvey SD, Radune D, Bergman NH, Phillippy AM. Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biology 14:R101 2013.

KmerGenie: Chikhi, R, Medvedev, P. Informed and Automated k-Mer Size Selection for Genome Assembly. Bioinformatics btt310, 2013.


SPAdes: Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. Alekseyev, and Pavel A. Pevzner. Journal of Computational Biology. May 2012, 19(5): 455-477. doi:10.1089/cmb.2012.0021.

Edena: Hernandez D, Tewhey R, Veyrieras J, Farinelli L, Østerås M, François P, and Schrenzel J. De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads. Bioinformatics, btt590, 2013.

SOAPdenovo: Li Y, Hu Y, Bolund L, Wang J: State of the art de novo assembly of human genomes from massively parallel sequencing data.Human genomics 2010, 4:271-277.

SOAPdenovo2: Luo, R, Liu, B, Xie, Y, Li, Z, Huang, W, Yuan, J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu S, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam T, Wang J. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience, 1(1), 18, 2012.

IDBA-UD: Peng, Y., Leung, H. C., Yiu, S. M., & Chin, F. Y. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics, 28(11), 1420-1428, 2012.

Meta-IDBA: Peng Y, Leung HCM, Yiu SM, Chin FYL: Meta-IDBA: a de Novo assembler for metagenomic data. Bioinformatics 2011, 27:i94-i101.

Velvet: Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008 May;18(5):821-9.

MetaVelvet: Namiki, T., Hachiya, T., Tanaka, H., & Sakakibara, Y. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic acids research, 40(20), e155-e155, 2012.

Celera Assembler: Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G. Aggressive assembly of pyrosequencing reads with mates.Bioinformatics. 2008 Dec 15;24(24):2818-24. Epub 2008 Oct 24.

Minimus: Sommer DD, Delcher AL, Salzberg SL, Pop M. Minimus: a fast, lightweight genome assembler. BMC Bioinformatics. 2007 Feb 26;8:64.

Sparse Assembler: Ye C, Ma ZS, Cannon CH, Pop M, Yu DW. Exploiting sparseness in de novo genome assembly. BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S1.

Velvet-SC: Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner PA, Lasken RL. Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nature Biotechnology, vol. 29, no. 11, pp. 915-921 (2011)

MaSuRCA: Zimin, A, Marçais, G, Puiu, D, Roberts, M, Salzberg, SL, Yorke, JA. The MaSuRCA genome assembler. Bioinformatics, btt476, 2013.

Ray: Boisvert, S, Raymond, F, Godzaridis, É, Laviolette, F, Corbeil, J. Ray Meta: scalable de novo metagenome assembly and profiling. Genome biology, 13(12), R122, 2013.

ABySS: Simpson, JT, Wong, K, Jackman, SD, Schein, JE, Jones, SJ, Birol, İ. ABySS: a parallel assembler for short read sequence data. Genome research, 19(6), 1117-1123, 2009.

SGA: Simpson, JT, Durbin, R. Efficient de novo assembly of large genomes using compressed data structures. Genome Research, 22(3), 549-556, 2012.

MIRA: Chevreux, B, Wetter, T, Suhai, S. Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. In German Conference on Bioinformatics (pp. 45-56), 1999.

Read Mapping

Bowtie: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. Epub 2009 Mar 4.

Bowtie2: Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012 Mar 4;9(4):357-9. doi: 10.1038/nmeth.1923.


FCP,Naive Bayesian Classifier: Macdonald NJ, Parks DH, Beiko RG. Rapid identification of high-confidence taxonomic assignments for metagenomic data. Nucleic Acids Res. 2012 Apr 24.

BLAST: Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403-10.

PHMMER: Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol. 2011 Oct;7(10):e1002195. Epub 2011 Oct 20.

PHYMM: Brady A, Salzberg SL. PhymmBL expanded: confidence scores, custom databases, parallelization and more. Nat Methods. 2011 May;8(5):367.

PhyloSift: Darling, AE, Jospin, G, Lowe, E, Matsen IV, FA, Bik, HM, Eisen, JA. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ, 2, e243, 2014.

MetaPhyler: Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M. Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics. 2011;12 Suppl 2:S4. Epub 2011 Jul 27.

Kraken: Wood DE, Salzberg SL: Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biology 2014, 15:R46.


FragGeneScan: Rho M, Tang H, Ye Y: FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Research 2010, 38:e191-e191.

MetaGeneMark: Borodovsky M, Mills R, Besemer J, Lomsadze A: Prokaryotic gene prediction using GeneMark and GeneMark.hmm.Current protocols in bioinformatics editoral board Andreas D Baxevanis et al 2003, Chapter 4:Unit4.6-Unit4.6.

Prokka: Prokka: Prokaryotic Genome Annotation System -

Glimmer-MG: Kelley DR, Liu B, Delcher AL, Pop M, Salzberg SL. Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. Nucleic Acids Res. 2012 Jan;40(1):e9. Epub 2011 Nov 18.


LAP: Ghodsi M, Hill CM, Astrovskaya I, Lin H, Sommer DD, Koren S, Pop M. De novo likelihood-based measures for comparing genome assemblies. BMC research notes 6:334, 2013.

ALE: Clark, SC, Egan, R, Frazier, PI, Wang, Z. ALE: a generic assembly likelihood evaluation framework for assessing

the accuracy of genome and metagenome assemblies. Bioinformatics, 29(4) 435-443, 2013.

QUAST: Gurevich, A, Saveliev, V, Vyahhi, N, Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics, 29(8), 1072-1075, 2013.

FRCbam: Vezzi, F, Narzisi, G, Mishra, B. Reevaluating assembly evaluations with feature response curves: GAGE and assemblathons. PloS ONE, 7(12), e52210, 2013.

CGAL: Rahman, A, Pachter, L CGAL: computing genome assembly likelihoods. Genome biology, 14(1), R8, 2013.

FreeBayes: Garrison, E, Marth, G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907, 2012.

REAPR: Hunt, M, Kikuchi, T, Sanders, M, Newbold, C, Berriman, M, & Otto, TD. REAPR: a universal tool for genome assembly evaluation. Genome biology, 14(5), R47, 2013.


Bambus 2: Koren S, Treangen TJ, Pop M. Bambus 2: scaffolding metagenomes. Bioinformatics 27(21): 2964-2971 2011.


M-GCAT: Treangen TJ, Messeguer X. M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. BMC Bioinformatics, 2006.

SAMtools: Li H., Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9

Krona: Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30;12:385.