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97 Metagenomics Classifiers…

And growing… 

Below is a simple bibliography of metagenomics classification algorithms, built from the GoogleDoc I created some time ago (2015?) and now maintained over at Zotero. So far, I’ve identified 97 (!!!) papers that all are trying to solve the same problem: what is in this sample?

It’s pretty incredible – I wonder at how many newly minted PhDs are represented in this list. If I put a more skeptical hat on, I also wonder whether the community is chasing an classification-prediction asymptote, and whether we are well past the point of “Good Enough“. Should algo developers perhaps focus on other aspects of the question above (for example, what makes a database “good enough” and how does it affect the algo used for classification?). 

PLEASE NOTE: I know I’ve missed some references below – so please lend a helping hand and leave a comment here to point me to something I may have. I’ll add whatever paper you link to my Zotero bibliography and update this in the future.

  1. Ahn, Tae-Hyuk, Juanjuan Chai, and Chongle Pan. “Sigma: Strain-Level Inference of Genomes from Metagenomic Analysis for Biosurveillance.” Bioinformatics 31, no. 2 (January 15, 2015): 170–77. https://doi.org/10.1093/bioinformatics/btu641.
  2. Ai, Dongmei, Ruocheng Huang, Jin Wen, Chao Li, Jiangping Zhu, and Li Charlie Xia. “Integrated Metagenomic Data Analysis Demonstrates That a Loss of Diversity in Oral Microbiota Is Associated with Periodontitis.” BMC Genomics 18, no. S1 (January 2017). https://doi.org/10.1186/s12864-016-3254-5.
  3. Ainsworth, David, Michael J. E. Sternberg, Come Raczy, and Sarah A. Butcher. “K-SLAM: Accurate and Ultra-Fast Taxonomic Classification and Gene Identification for Large Metagenomic Data Sets.” Nucleic Acids Research 45, no. 4 (28 2017): 1649–56. https://doi.org/10.1093/nar/gkw1248.
  4. Ames, Sasha K., David A. Hysom, Shea N. Gardner, G. Scott Lloyd, Maya B. Gokhale, and Jonathan E. Allen. “Scalable Metagenomic Taxonomy Classification Using a Reference Genome Database.” Bioinformatics 29, no. 18 (September 15, 2013): 2253–60. https://doi.org/10.1093/bioinformatics/btt389.
  5. Ander, Christina, Ole B. Schulz-Trieglaff, Jens Stoye, and Anthony J. Cox. “MetaBEETL: High-Throughput Analysis of Heterogeneous Microbial Populations from Shotgun DNA Sequences.” BMC Bioinformatics 14 Suppl 5 (2013): S2. https://doi.org/10.1186/1471-2105-14-S5-S2.
  6. Andrusch, Andreas, Piotr W. Dabrowski, Jeanette Klenner, Simon H. Tausch, Claudia Kohl, Abdalla A. Osman, Bernhard Y. Renard, and Andreas Nitsche. “PAIPline: Pathogen Identification in Metagenomic and Clinical next Generation Sequencing Samples.” Bioinformatics (Oxford, England) 34, no. 17 (September 1, 2018): i715–21. https://doi.org/10.1093/bioinformatics/bty595.
  7. Angiuoli, Samuel V, Malcolm Matalka, Aaron Gussman, Kevin Galens, Mahesh Vangala, David R Riley, Cesar Arze, James R White, Owen White, and W Florian Fricke. “CloVR: A Virtual Machine for Automated and Portable Sequence Analysis from the Desktop Using Cloud Computing.” BMC Bioinformatics 12, no. 1 (2011): 356. https://doi.org/10.1186/1471-2105-12-356.
  8. Bayliss, Sion C., Aravind Sankar, Edward J. Feil, Jukka Corander, Ben Pascoe, Guillaume Méric, Antti Honkela, Matthew D. Hitchings, Brandon Malone, and Samuel K. Sheppard. “Bayesian Identification of Bacterial Strains from Sequencing Data.” Microbial Genomics 2, no. 8 (August 25, 2016). https://doi.org/10.1099/mgen.0.000075.
  9. Berendzen, Joel, William J Bruno, Judith D Cohn, Nicolas W Hengartner, Cheryl R Kuske, Benjamin H McMahon, Murray A Wolinsky, and Gary Xie. “Rapid Phylogenetic and Functional Classification of Short Genomic Fragments with Signature Peptides.” BMC Research Notes 5, no. 1 (2012): 460. https://doi.org/10.1186/1756-0500-5-460.
  10. Brady, Arthur, and Steven Salzberg. “PhymmBL Expanded: Confidence Scores, Custom Databases, Parallelization and More.” Nature Methods 8, no. 5 (May 2011): 367. https://doi.org/10.1038/nmeth0511-367.
  11. Brady, Arthur, and Steven L. Salzberg. “Phymm and PhymmBL: Metagenomic Phylogenetic Classification with Interpolated Markov Models.” Nature Methods 6, no. 9 (September 2009): 673–76. https://doi.org/10.1038/nmeth.1358.
  12. Breitwieser, F. P., D. N. Baker, and S. L. Salzberg. “KrakenUniq: Confident and Fast Metagenomics Classification Using Unique k-Mer Counts.” Genome Biology 19, no. 1 (November 16, 2018): 198. https://doi.org/10.1186/s13059-018-1568-0.
  13. Břinda, Karel, Kamil Salikhov, Simone Pignotti, and Gregory Kucherov. “Karel-Brinda/Prophyle: Prophyle 0.3.0.3.” Zenodo, November 11, 2017. https://doi.org/10.5281/zenodo.1045429.
  14. Břinda, Karel, Maciej Sykulski, and Gregory Kucherov. “Spaced Seeds Improve k -Mer-Based Metagenomic Classification.” Bioinformatics 31, no. 22 (November 15, 2015): 3584–92. https://doi.org/10.1093/bioinformatics/btv419.
  15. Cai, Lin, and Tong Zhang. “Detecting Human Bacterial Pathogens in Wastewater Treatment Plants by a High-Throughput Shotgun Sequencing Technique.” Environmental Science & Technology 47, no. 10 (May 21, 2013): 5433–41. https://doi.org/10.1021/es400275r.
  16. Caporaso, J. Gregory, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D. Bushman, Elizabeth K. Costello, Noah Fierer, et al. “QIIME Allows Analysis of High-Throughput Community Sequencing Data.” Nature Methods 7, no. 5 (May 2010): 335–36. https://doi.org/10.1038/nmeth.f.303.
  17. Corvelo, André, Wayne E. Clarke, Nicolas Robine, and Michael C. Zody. “TaxMaps: Comprehensive and Highly Accurate Taxonomic Classification of Short-Read Data in Reasonable Time.” Genome Research 28, no. 5 (May 2018): 751–58. https://doi.org/10.1101/gr.225276.117.
  18. Cosentino, Salvatore, Mette Voldby Larsen, Frank Møller Aarestrup, and Ole Lund. “PathogenFinder – Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data.” Edited by Jason D. Barbour. PLoS ONE 8, no. 10 (October 28, 2013): e77302. https://doi.org/10.1371/journal.pone.0077302.
  19. Dadi, Temesgen Hailemariam, Bernhard Y. Renard, Lothar H. Wieler, Torsten Semmler, and Knut Reinert. “SLIMM: Species Level Identification of Microorganisms from Metagenomes.” PeerJ 5 (March 28, 2017): e3138. https://doi.org/10.7717/peerj.3138.
  20. Darling, Aaron E., Guillaume Jospin, Eric Lowe, Frederick A. Matsen, Holly M. Bik, and Jonathan A. Eisen. “PhyloSift: Phylogenetic Analysis of Genomes and Metagenomes.” PeerJ 2 (2014): e243. https://doi.org/10.7717/peerj.243.
  21. Davenport, Colin F., Jens Neugebauer, Nils Beckmann, Benedikt Friedrich, Burim Kameri, Svea Kokott, Malte Paetow, et al. “Genometa – A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads.” Edited by Niall James Haslam. PLoS ONE 7, no. 8 (August 21, 2012): e41224. https://doi.org/10.1371/journal.pone.0041224.
  22. Deneke, Carlus, Robert Rentzsch, and Bernhard Y. Renard. “PaPrBaG: A Machine Learning Approach for the Detection of Novel Pathogens from NGS Data.” Scientific Reports 7 (04 2017): 39194. https://doi.org/10.1038/srep39194.
  23. Edwards, Robert A., Robert Olson, Terry Disz, Gordon D. Pusch, Veronika Vonstein, Rick Stevens, and Ross Overbeek. “Real Time Metagenomics: Using k-Mers to Annotate Metagenomes.” Bioinformatics (Oxford, England) 28, no. 24 (December 15, 2012): 3316–17. https://doi.org/10.1093/bioinformatics/bts599.
  24. Fischer, Martina, Benjamin Strauch, and Bernhard Y. Renard. “Abundance Estimation and Differential Testing on Strain Level in Metagenomics Data.” Bioinformatics (Oxford, England) 33, no. 14 (July 15, 2017): i124–32. https://doi.org/10.1093/bioinformatics/btx237.
  25. Flygare, Steven, Keith Simmon, Chase Miller, Yi Qiao, Brett Kennedy, Tonya Di Sera, Erin H. Graf, et al. “Taxonomer: An Interactive Metagenomics Analysis Portal for Universal Pathogen Detection and Host MRNA Expression Profiling.” Genome Biology 17, no. 1 (26 2016): 111. https://doi.org/10.1186/s13059-016-0969-1.
  26. Freitas, Tracey Allen K., Po-E. Li, Matthew B. Scholz, and Patrick S. G. Chain. “Accurate Read-Based Metagenome Characterization Using a Hierarchical Suite of Unique Signatures.” Nucleic Acids Research 43, no. 10 (May 26, 2015): e69. https://doi.org/10.1093/nar/gkv180.
  27. Gerlach, Wolfgang, and Jens Stoye. “Taxonomic Classification of Metagenomic Shotgun Sequences with CARMA3.” Nucleic Acids Research 39, no. 14 (August 2011): e91. https://doi.org/10.1093/nar/gkr225.
  28. Gori, Fabio, Gianluigi Folino, Mike S. M. Jetten, and Elena Marchiori. “MTR: Taxonomic Annotation of Short Metagenomic Reads Using Clustering at Multiple Taxonomic Ranks.” Bioinformatics (Oxford, England) 27, no. 2 (January 15, 2011): 196–203. https://doi.org/10.1093/bioinformatics/btq649.
  29. Gregor, Ivan, Johannes Dröge, Melanie Schirmer, Christopher Quince, and Alice C. McHardy. “PhyloPythiaS+: A Self-Training Method for the Rapid Reconstruction of Low-Ranking Taxonomic Bins from Metagenomes.” PeerJ 4 (2016): e1603. https://doi.org/10.7717/peerj.1603.
  30. Greninger, Alexander L., Samia N. Naccache, Scot Federman, Guixia Yu, Placide Mbala, Vanessa Bres, Doug Stryke, et al. “Rapid Metagenomic Identification of Viral Pathogens in Clinical Samples by Real-Time Nanopore Sequencing Analysis.” Genome Medicine 7, no. 1 (December 2015). https://doi.org/10.1186/s13073-015-0220-9.
  31. Guan, Dengfeng, Bo Liu, and Yadong Wang. “DeSPI: Efficient Classification of Metagenomic Reads with Lightweight de Bruijn Graph-Based Reference Indexing,” October 11, 2016. https://doi.org/10.1101/080200.
  32. Hasman, H., D. Saputra, T. Sicheritz-Ponten, O. Lund, C. A. Svendsen, N. Frimodt-Moller, and F. M. Aarestrup. “Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples.” Journal of Clinical Microbiology 52, no. 1 (January 1, 2014): 139–46. https://doi.org/10.1128/JCM.02452-13.
  33. Hong, Changjin, Solaiappan Manimaran, Ying Shen, Joseph F. Perez-Rogers, Allyson L. Byrd, Eduardo Castro-Nallar, Keith A. Crandall, and William Evan Johnson. “PathoScope 2.0: A Complete Computational Framework for Strain Identification in Environmental or Clinical Sequencing Samples.” Microbiome 2 (2014): 33. https://doi.org/10.1186/2049-2618-2-33.
  34. Jain, Chirag, Alexander Dilthey, Sergey Koren, Srinivas Aluru, and Adam M. Phillippy. “A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases.” Journal of Computational Biology: A Journal of Computational Molecular Cell Biology 25, no. 7 (July 2018): 766–79. https://doi.org/10.1089/cmb.2018.0036.
  35. Kawulok, Jolanta, and Sebastian Deorowicz. “CoMeta: Classification of Metagenomes Using k-Mers.” PloS One 10, no. 4 (2015): e0121453. https://doi.org/10.1371/journal.pone.0121453.
  36. Kilianski, Andy, Patrick Carcel, Shijie Yao, Pierce Roth, Josh Schulte, Greg B. Donarum, Ed T. Fochler, et al. “Pathosphere.Org: Pathogen Detection and Characterization through a Web-Based, Open Source Informatics Platform.” BMC Bioinformatics 16, no. 1 (December 2015). https://doi.org/10.1186/s12859-015-0840-5.
  37. Kim, Daehwan, Li Song, Florian P. Breitwieser, and Steven L. Salzberg. “Centrifuge: Rapid and Sensitive Classification of Metagenomic Sequences.” Genome Research 26, no. 12 (2016): 1721–29. https://doi.org/10.1101/gr.210641.116.
  38. Kim, Minji, Xiejia Zhang, Jonathan G. Ligo, Farzad Farnoud, Venugopal V. Veeravalli, and Olgica Milenkovic. “MetaCRAM: An Integrated Pipeline for Metagenomic Taxonomy Identification and Compression.” BMC Bioinformatics 17 (February 19, 2016): 94. https://doi.org/10.1186/s12859-016-0932-x.
  39. Kisand, Veljo, Angelica Valente, Armin Lahm, Gerard Tanet, and Teresa Lettieri. “Phylogenetic and Functional Metagenomic Profiling for Assessing Microbial Biodiversity in Environmental Monitoring.” PloS One 7, no. 8 (2012): e43630. https://doi.org/10.1371/journal.pone.0043630.
  40. Klingenberg, Heiner, Kathrin Petra Aßhauer, Thomas Lingner, and Peter Meinicke. “Protein Signature-Based Estimation of Metagenomic Abundances Including All Domains of Life and Viruses.” Bioinformatics 29, no. 8 (April 15, 2013): 973–80. https://doi.org/10.1093/bioinformatics/btt077.
  41. Koslicki, David, and Daniel Falush. “MetaPalette: A k -Mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation.” Edited by Janet K. Jansson. MSystems 1, no. 3 (June 28, 2016). https://doi.org/10.1128/mSystems.00020-16.
  42. Koslicki, David, Simon Foucart, and Gail Rosen. “WGSQuikr: Fast Whole-Genome Shotgun Metagenomic Classification.” Edited by Mark R. Liles. PLoS ONE 9, no. 3 (March 13, 2014): e91784. https://doi.org/10.1371/journal.pone.0091784.
  43. Kostic, Aleksandar D., Akinyemi I. Ojesina, Chandra Sekhar Pedamallu, Joonil Jung, Roel G. W. Verhaak, Gad Getz, and Matthew Meyerson. “PathSeq: Software to Identify or Discover Microbes by Deep Sequencing of Human Tissue.” Nature Biotechnology 29, no. 5 (May 2011): 393–96. https://doi.org/10.1038/nbt.1868.
  44. Lindner, Martin S., and Bernhard Y. Renard. “Metagenomic Abundance Estimation and Diagnostic Testing on Species Level.” Nucleic Acids Research 41, no. 1 (January 7, 2013): e10. https://doi.org/10.1093/nar/gks803.
  45. Liu, Bo, Theodore Gibbons, Mohammad Ghodsi, and Mihai Pop. “MetaPhyler: Taxonomic Profiling for Metagenomic Sequences.” In 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 95–100. Hong Kong, China: IEEE, 2010. https://doi.org/10.1109/BIBM.2010.5706544.
  46. Liu, Bo, Theodore Gibbons, Mohammad Ghodsi, Todd Treangen, and Mihai Pop. “Accurate and Fast Estimation of Taxonomic Profiles from Metagenomic Shotgun Sequences.” BMC Genomics 12 Suppl 2 (2011): S4. https://doi.org/10.1186/1471-2164-12-S2-S4.
  47. Liu, Jiemeng, Haifeng Wang, Hongxing Yang, Yizhe Zhang, Jinfeng Wang, Fangqing Zhao, and Ji Qi. “Composition-Based Classification of Short Metagenomic Sequences Elucidates the Landscapes of Taxonomic and Functional Enrichment of Microorganisms.” Nucleic Acids Research 41, no. 1 (January 7, 2013): e3. https://doi.org/10.1093/nar/gks828.
  48. Liu, Xinan, Ye Yu, Jinpeng Liu, Corrine F. Elliott, Chen Qian, and Jinze Liu. “A Novel Data Structure to Support Ultra-Fast Taxonomic Classification of Metagenomic Sequences with k-Mer Signatures.” Bioinformatics (Oxford, England) 34, no. 1 (01 2018): 171–78. https://doi.org/10.1093/bioinformatics/btx432.
  49. Liu, Yongchao, Fabian Ripp, Rene Koeppel, Hanno Schmidt, Sören Lukas Hellmann, Mathias Weber, Christopher Felix Krombholz, Bertil Schmidt, and Thomas Hankeln. “AFS: Identification and Quantification of Species Composition by Metagenomic Sequencing.” Bioinformatics (Oxford, England) 33, no. 9 (01 2017): 1396–98. https://doi.org/10.1093/bioinformatics/btw822.
  50. Louvel, Guillaume, Clio Der Sarkissian, Kristian Hanghøj, and Ludovic Orlando. “MetaBIT, an Integrative and Automated Metagenomic Pipeline for Analysing Microbial Profiles from High-Throughput Sequencing Shotgun Data.” Molecular Ecology Resources 16, no. 6 (November 2016): 1415–27. https://doi.org/10.1111/1755-0998.12546.
  51. Lu, Jennifer, Florian P. Breitwieser, Peter Thielen, and Steven L. Salzberg. “Bracken: Estimating Species Abundance in Metagenomics Data.” PeerJ Computer Science 3 (January 2, 2017): e104. https://doi.org/10.7717/peerj-cs.104.
  52. Luo, Chengwei, Luis M. Rodriguez-R, and Konstantinos T. Konstantinidis. “MyTaxa: An Advanced Taxonomic Classifier for Genomic and Metagenomic Sequences.” Nucleic Acids Research 42, no. 8 (April 1, 2014): e73–e73. https://doi.org/10.1093/nar/gku169.
  53. MacDonald, Norman J., Donovan H. Parks, and Robert G. Beiko. “Rapid Identification of High-Confidence Taxonomic Assignments for Metagenomic Data.” Nucleic Acids Research 40, no. 14 (August 2012): e111. https://doi.org/10.1093/nar/gks335.
  54. Markowitz, Victor M., Natalia N. Ivanova, Ernest Szeto, Krishna Palaniappan, Ken Chu, Daniel Dalevi, I.-Min A. Chen, et al. “IMG/M: A Data Management and Analysis System for Metagenomes.” Nucleic Acids Research 36, no. Database issue (January 2008): D534-538. https://doi.org/10.1093/nar/gkm869.
  55. McIntyre, Alexa B. R., Rachid Ounit, Ebrahim Afshinnekoo, Robert J. Prill, Elizabeth Hénaff, Noah Alexander, Samuel S. Minot, et al. “Comprehensive Benchmarking and Ensemble Approaches for Metagenomic Classifiers.” Genome Biology 18, no. 1 (21 2017): 182. https://doi.org/10.1186/s13059-017-1299-7.
  56. Meinicke, Peter, Kathrin Petra Aßhauer, and Thomas Lingner. “Mixture Models for Analysis of the Taxonomic Composition of Metagenomes.” Bioinformatics 27, no. 12 (June 15, 2011): 1618–24. https://doi.org/10.1093/bioinformatics/btr266.
  57. Mende, Daniel R., Shinichi Sunagawa, Georg Zeller, and Peer Bork. “Accurate and Universal Delineation of Prokaryotic Species.” Nature Methods 10, no. 9 (September 2013): 881–84. https://doi.org/10.1038/nmeth.2575.
  58. Menzel, Peter, Kim Lee Ng, and Anders Krogh. “Fast and Sensitive Taxonomic Classification for Metagenomics with Kaiju.” Nature Communications 7 (April 13, 2016): 11257. https://doi.org/10.1038/ncomms11257.
  59. Meyer, F., D. Paarmann, M. D’Souza, R. Olson, E. M. Glass, M. Kubal, T. Paczian, et al. “The Metagenomics RAST Server – a Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes.” BMC Bioinformatics 9 (September 19, 2008): 386. https://doi.org/10.1186/1471-2105-9-386.
  60. Mohammed, Monzoorul Haque, Sudha Chadaram, Dinakar Komanduri, Tarini Shankar Ghosh, and Sharmila S. Mande. “Eu-Detect: An Algorithm for Detecting Eukaryotic Sequences in Metagenomic Data Sets.” Journal of Biosciences 36, no. 4 (September 2011): 709–17.
  61. Monzoorul Haque, M., Tarini Shankar Ghosh, Dinakar Komanduri, and Sharmila S. Mande. “SOrt-ITEMS: Sequence Orthology Based Approach for Improved Taxonomic Estimation of Metagenomic Sequences.” Bioinformatics (Oxford, England) 25, no. 14 (July 15, 2009): 1722–30. https://doi.org/10.1093/bioinformatics/btp317.
  62. Morfopoulou, Sofia, and Vincent Plagnol. “Bayesian Mixture Analysis for Metagenomic Community Profiling.” Bioinformatics (Oxford, England) 31, no. 18 (September 15, 2015): 2930–38. https://doi.org/10.1093/bioinformatics/btv317.
  63. Naccache, S. N., S. Federman, N. Veeraraghavan, M. Zaharia, D. Lee, E. Samayoa, J. Bouquet, et al. “A Cloud-Compatible Bioinformatics Pipeline for Ultrarapid Pathogen Identification from next-Generation Sequencing of Clinical Samples.” Genome Research 24, no. 7 (July 1, 2014): 1180–92. https://doi.org/10.1101/gr.171934.113.
  64. Naeem, Raeece, Mamoon Rashid, and Arnab Pain. “READSCAN: A Fast and Scalable Pathogen Discovery Program with Accurate Genome Relative Abundance Estimation.” Bioinformatics 29, no. 3 (February 1, 2013): 391–92. https://doi.org/10.1093/bioinformatics/bts684.
  65. Nalbantoglu, Ozkan U., Samuel F. Way, Steven H. Hinrichs, and Khalid Sayood. “RAIphy: Phylogenetic Classification of Metagenomics Samples Using Iterative Refinement of Relative Abundance Index Profiles.” BMC Bioinformatics 12 (January 31, 2011): 41. https://doi.org/10.1186/1471-2105-12-41.
  66. Nazeen, Sumaiya, and Bonnie Berger. “Carnelian: Alignment-Free Functional Binning and Abundance Estimation of Metagenomic Reads,” July 23, 2018. https://doi.org/10.1101/375121.
  67. Nguyen, Nam-Phuong, Siavash Mirarab, Bo Liu, Mihai Pop, and Tandy Warnow. “TIPP: Taxonomic Identification and Phylogenetic Profiling.” Bioinformatics (Oxford, England) 30, no. 24 (December 15, 2014): 3548–55. https://doi.org/10.1093/bioinformatics/btu721.
  68. Niu, Beifang, Zhengwei Zhu, Limin Fu, Sitao Wu, and Weizhong Li. “FR-HIT, a Very Fast Program to Recruit Metagenomic Reads to Homologous Reference Genomes.” Bioinformatics (Oxford, England) 27, no. 12 (June 15, 2011): 1704–5. https://doi.org/10.1093/bioinformatics/btr252.
  69. Ounit, Rachid, and Stefano Lonardi. “Higher Classification Sensitivity of Short Metagenomic Reads with CLARK-S.” Bioinformatics (Oxford, England) 32, no. 24 (15 2016): 3823–25. https://doi.org/10.1093/bioinformatics/btw542.
  70. Ounit, Rachid, Steve Wanamaker, Timothy J. Close, and Stefano Lonardi. “CLARK: Fast and Accurate Classification of Metagenomic and Genomic Sequences Using Discriminative k-Mers.” BMC Genomics 16 (March 25, 2015): 236. https://doi.org/10.1186/s12864-015-1419-2.
  71. Patil, Kaustubh Raosaheb, Linus Roune, and Alice Carolyn McHardy. “The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences.” PloS One 7, no. 6 (2012): e38581. https://doi.org/10.1371/journal.pone.0038581.
  72. Petersen, Thomas Nordahl, Oksana Lukjancenko, Martin Christen Frølund Thomsen, Maria Maddalena Sperotto, Ole Lund, Frank Møller Aarestrup, and Thomas Sicheritz-Pontén. “MGmapper: Reference Based Mapping and Taxonomy Annotation of Metagenomics Sequence Reads.” Edited by Lingling An. PLOS ONE 12, no. 5 (May 3, 2017): e0176469. https://doi.org/10.1371/journal.pone.0176469.
  73. Piro, Vitor C., Martin S. Lindner, and Bernhard Y. Renard. “DUDes: A Top-down Taxonomic Profiler for Metagenomics.” Bioinformatics (Oxford, England) 32, no. 15 (01 2016): 2272–80. https://doi.org/10.1093/bioinformatics/btw150.
  74. Porter, Michael S., and Robert G. Beiko. “SPANNER: Taxonomic Assignment of Sequences Using Pyramid Matching of Similarity Profiles.” Bioinformatics (Oxford, England) 29, no. 15 (August 1, 2013): 1858–64. https://doi.org/10.1093/bioinformatics/btt313.
  75. Rawat, Arun, David M. Engelthaler, Elizabeth M. Driebe, Paul Keim, and Jeffrey T. Foster. “MetaGeniE: Characterizing Human Clinical Samples Using Deep Metagenomic Sequencing.” PloS One 9, no. 11 (2014): e110915. https://doi.org/10.1371/journal.pone.0110915.
  76. Reppell, Mark, and John Novembre. “Using Pseudoalignment and Base Quality to Accurately Quantify Microbial Community Composition.” Edited by Alice Carolyn McHardy. PLOS Computational Biology 14, no. 4 (April 16, 2018): e1006096. https://doi.org/10.1371/journal.pcbi.1006096.
  77. Roberts, Adam, and Lior Pachter. “Streaming Fragment Assignment for Real-Time Analysis of Sequencing Experiments.” Nature Methods 10, no. 1 (January 2013): 71–73. https://doi.org/10.1038/nmeth.2251.
  78. Rosen, Gail L., and Tze Yee Lim. “NBC Update: The Addition of Viral and Fungal Databases to the Naïve Bayes Classification Tool.” BMC Research Notes 5 (January 31, 2012): 81. https://doi.org/10.1186/1756-0500-5-81.
  79. Rosen, Gail L., Erin R. Reichenberger, and Aaron M. Rosenfeld. “NBC: The Naive Bayes Classification Tool Webserver for Taxonomic Classification of Metagenomic Reads.” Bioinformatics (Oxford, England) 27, no. 1 (January 1, 2011): 127–29. https://doi.org/10.1093/bioinformatics/btq619.
  80. Schaeffer, L., H. Pimentel, N. Bray, P. Melsted, and L. Pachter. “Pseudoalignment for Metagenomic Read Assignment.” Bioinformatics (Oxford, England) 33, no. 14 (July 15, 2017): 2082–88. https://doi.org/10.1093/bioinformatics/btx106.
  81. Scheuch, Matthias, Dirk Höper, and Martin Beer. “RIEMS: A Software Pipeline for Sensitive and Comprehensive Taxonomic Classification of Reads from Metagenomics Datasets.” BMC Bioinformatics 16 (March 3, 2015): 69. https://doi.org/10.1186/s12859-015-0503-6.
  82. Schloss, Patrick D., Sarah L. Westcott, Thomas Ryabin, Justine R. Hall, Martin Hartmann, Emily B. Hollister, Ryan A. Lesniewski, et al. “Introducing Mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities.” Applied and Environmental Microbiology 75, no. 23 (December 2009): 7537–41. https://doi.org/10.1128/AEM.01541-09.
  83. Segata, Nicola, Levi Waldron, Annalisa Ballarini, Vagheesh Narasimhan, Olivier Jousson, and Curtis Huttenhower. “Metagenomic Microbial Community Profiling Using Unique Clade-Specific Marker Genes.” Nature Methods 9, no. 8 (June 10, 2012): 811–14. https://doi.org/10.1038/nmeth.2066.
  84. Shamsaddini, Amirhossein, Yang Pan, W. Evan Johnson, Konstantinos Krampis, Mariya Shcheglovitova, Vahan Simonyan, Amy Zanne, and Raja Mazumder. “Census-Based Rapid and Accurate Metagenome Taxonomic Profiling.” BMC Genomics 15 (October 21, 2014): 918. https://doi.org/10.1186/1471-2164-15-918.
  85. Sharma, Vineet K., Naveen Kumar, Tulika Prakash, and Todd D. Taylor. “Fast and Accurate Taxonomic Assignments of Metagenomic Sequences Using MetaBin.” PloS One 7, no. 4 (2012): e34030. https://doi.org/10.1371/journal.pone.0034030.
  86. Sunagawa, Shinichi, Daniel R. Mende, Georg Zeller, Fernando Izquierdo-Carrasco, Simon A. Berger, Jens Roat Kultima, Luis Pedro Coelho, et al. “Metagenomic Species Profiling Using Universal Phylogenetic Marker Genes.” Nature Methods 10, no. 12 (December 2013): 1196–99. https://doi.org/10.1038/nmeth.2693.
  87. Takeuchi, Fumihiko, Tsuyoshi Sekizuka, Akifumi Yamashita, Yumiko Ogasawara, Katsumi Mizuta, and Makoto Kuroda. “MePIC, Metagenomic Pathogen Identification for Clinical Specimens.” Japanese Journal of Infectious Diseases 67, no. 1 (2014): 62–65. https://doi.org/10.7883/yoken.67.62.
  88. Truong, Duy Tin, Eric A. Franzosa, Timothy L. Tickle, Matthias Scholz, George Weingart, Edoardo Pasolli, Adrian Tett, Curtis Huttenhower, and Nicola Segata. “MetaPhlAn2 for Enhanced Metagenomic Taxonomic Profiling.” Nature Methods 12, no. 10 (October 2015): 902–3. https://doi.org/10.1038/nmeth.3589.
  89. Truong, Duy Tin, Adrian Tett, Edoardo Pasolli, Curtis Huttenhower, and Nicola Segata. “Microbial Strain-Level Population Structure and Genetic Diversity from Metagenomes.” Genome Research 27, no. 4 (2017): 626–38. https://doi.org/10.1101/gr.216242.116.
  90. Tu, Qichao, Zhili He, and Jizhong Zhou. “Strain/Species Identification in Metagenomes Using Genome-Specific Markers.” Nucleic Acids Research 42, no. 8 (April 1, 2014): e67–e67. https://doi.org/10.1093/nar/gku138.
  91. Westbrook, Anthony, Jordan Ramsdell, Taruna Schuelke, Louisa Normington, R. Daniel Bergeron, W. Kelley Thomas, and Matthew D. MacManes. “PALADIN: Protein Alignment for Functional Profiling Whole Metagenome Shotgun Data.” Bioinformatics (Oxford, England) 33, no. 10 (May 15, 2017): 1473–78. https://doi.org/10.1093/bioinformatics/btx021.
  92. Wood, Derrick E., and Steven L. Salzberg. “Kraken: Ultrafast Metagenomic Sequence Classification Using Exact Alignments.” Genome Biology 15, no. 3 (March 3, 2014): R46. https://doi.org/10.1186/gb-2014-15-3-r46.
  93. Xia, Li C., Jacob A. Cram, Ting Chen, Jed A. Fuhrman, and Fengzhu Sun. “Accurate Genome Relative Abundance Estimation Based on Shotgun Metagenomic Reads.” Edited by Emmanuel Dias-Neto. PLoS ONE 6, no. 12 (December 6, 2011): e27992. https://doi.org/10.1371/journal.pone.0027992.
  94. Zhang, Zheng, Scott Schwartz, Lukas Wagner, and Webb Miller. “A Greedy Algorithm for Aligning DNA Sequences.” Journal of Computational Biology 7, no. 1–2 (February 2000): 203–14. https://doi.org/10.1089/10665270050081478.
  95. Zhao, Guoyan, Guang Wu, Efrem S. Lim, Lindsay Droit, Siddharth Krishnamurthy, Dan H. Barouch, Herbert W. Virgin, and David Wang. “VirusSeeker, a Computational Pipeline for Virus Discovery and Virome Composition Analysis.” Virology 503 (2017): 21–30. https://doi.org/10.1016/j.virol.2017.01.005.
  96. Zhou, Wei, Ruilin Li, Shuo Yuan, ChangChun Liu, Shaowen Yao, Jing Luo, and Beifang Niu. “MetaSpark: A Spark-Based Distributed Processing Tool to Recruit Metagenomic Reads to Reference Genomes.” Bioinformatics (Oxford, England) 33, no. 7 (01 2017): 1090–92. https://doi.org/10.1093/bioinformatics/btw750.
  97. Zolfo, Moreno, Adrian Tett, Olivier Jousson, Claudio Donati, and Nicola Segata. “MetaMLST: Multi-Locus Strain-Level Bacterial Typing from Metagenomic Samples.” Nucleic Acids Research 45, no. 2 (25 2017): e7. https://doi.org/10.1093/nar/gkw837.

Published by Jonathan Jacobs

You can catch up with Jonathan on Twitter (@bioinformer).

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