metAMOS configuration summary: metAMOS Version: v1.5rc1 Praline Brownie workflows: core,imetamos Time and Date: 2013-11-06 Working directory: /panfs/nbacc1/project/fy14/iMetAMOS/test_isolate Prefix: proba K-Mer: 25,35,45,55,65,75,85,95,105,125 Threads: 32 Taxonomic level: genus Verbose: True Steps to skip: FindRepeats, Scaffold, Propagate, Propagate Steps to force: [citation] metAMOS Treangen, TJ ⇔ Koren, S, Sommer, DD, Liu, B, Astrovskaya, I, Ondov, B, Darling AE, Phillippy AM, Pop, M. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome biology, 14(1), R2, 2013. iMetAMOS Koren, S, Treangen, TJ, Hill, CM, Pop, M, Phillippy, AM. Automated ensemble assembly and validation of microbial genomes. In prep. Step-specific configuration: [abundance] MetaPhyler /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64 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. [multialign] M-GCAT /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64 Treangen TJ, Messeguer X. M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. BMC Bioinformatics, 2006. [fannotate] BLAST /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64 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. [scaffold] Bambus 2 /panfs/nbacc1/local/packages/iMetAMOS/AMOS/Linux-x86_64/bin Koren S, Treangen TJ, Pop M. Bambus 2: scaffolding metagenomes. Bioinformatics 27(21): 2964-2971 2011. [findorfs] Prokka /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin Prokka: Prokaryotic Genome Annotation System - http://vicbioinformatics.com/ [annotate] Kraken /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/kraken/bin Wood DE, Salzberg SL. Rapid phylogenetic sequence classification through repeated exact alignment. In preparation. [mapreads] Bowtie /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64 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. [assemble] ABySS /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/abyss/bin 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. SPAdes /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/spades/bin 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. MIRA /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/mira/bin 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. SOAPdenovo2 /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/soap2/bin 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. Velvet /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/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. Epub 2008 Mar 18. SGA /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/sga/bin Simpson, JT, Durbin, R. Efficient de novo assembly of large genomes using compressed data structures. Genome Research, 22(3), 549-556, 2012. IDBA-UD /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/idba/bin 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. MaSuRCA /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/MaSuRCA/bin Zimin, A, Marçais, G, Puiu, D, Roberts, M, Salzberg, SL, Yorke, JA. The MaSuRCA genome assembler. Bioinformatics, btt476, 2013. Velvet-SC /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/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) Sparse Assembler /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/SparseAssembler 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. Ray /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/Ray/bin 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. [validate] FRCbam /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/FRCbam/bin Vezzi, F, Narzisi, G, Mishra, B. Reevaluating assembly evaluations with feature response curves: GAGE and assemblathons. PloS ONE, 7(12), e52210, 2013. CGAL /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/cgal Rahman, A, Pachter, L CGAL: computing genome assembly likelihoods. Genome biology, 14(1), R8, 2013. ALE /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/ALE/src 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 /panfs/nbacc1/local/packages/iMetAMOS/quast Gurevich, A, Saveliev, V, Vyahhi, N, Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics, 29(8), 1072-1075, 2013. Prokka /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/prokka/bin Prokka: Prokaryotic Genome Annotation System - http://vicbioinformatics.com/ FreeBayes /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/freebayes/bin Garrison, E, Marth, G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907, 2012. LAP /panfs/nbacc1/local/packages/iMetAMOS/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. REAPR /panfs/nbacc1/local/packages/iMetAMOS/Utilities/cpp/Linux-x86_64/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. [other] Krona /panfs/nbacc1/local/packages/iMetAMOS/KronaTools/bin Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30;12:385.