References

NanoClass2 makes use of third-party software and resources. If you make use of NanoClass2 we recommend that you cite this software as well.

The version numbers are the exact versions used to develop this workflow.

Database

Software

References

Allard, Guy, Feargal J. Ryan, Ian B. Jeffery, and Marcus J. Claesson. 2015. “SPINGO: A Rapid Species-Classifier for Microbial Amplicon Sequences.” BMC Bioinformatics 16 (1): 324. https://doi.org/10.1186/s12859-015-0747-1.
Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. “Basic local alignment search tool.” Journal of Molecular Biology 215 (3): 403–10. https://doi.org/10.1016/S0022-2836(05)80360-2.
De Coster, Wouter, Svenn D’Hert, Darrin T Schultz, Marc Cruts, and Christine Van Broeckhoven. 2018. “NanoPack: Visualizing and Processing Long-Read Sequencing Data.” Bioinformatics 34 (15): 2666–69. https://doi.org/10.1093/bioinformatics/bty149.
De Coster, Wouter, and Rosa Rademakers. 2023. “NanoPack2: Population-Scale Evaluation of Long-Read Sequencing Data.” Bioinformatics 39 (5): btad311. https://doi.org/10.1093/bioinformatics/btad311.
Estaki, Mehrbod, Lingjing Jiang, Nicholas A. Bokulich, Daniel McDonald, Antonio González, Tomasz Kosciolek, Cameron Martino, et al. 2020. “QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data.” Current Protocols in Bioinformatics 70 (1): e100. https://doi.org/10.1002/cpbi.100.
Kim, Daehwan, Li Song, Florian P. Breitwieser, and Steven L. Salzberg. 2016. “Centrifuge: Rapid and Sensitive Classification of Metagenomic Sequences.” Genome Research 26 (12): 1721–29. https://doi.org/10.1101/gr.210641.116.
Li, Heng. 2018. “Minimap2: Pairwise Alignment for Nucleotide Sequences.” Bioinformatics 34 (18): 3094–3100. https://doi.org/10.1093/bioinformatics/bty191.
Li, Heng, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, and Richard Durbin. 2009. “The Sequence Alignment/Map Format and SAMtools.” Bioinformatics 25 (16): 2078–79. https://doi.org/10.1093/bioinformatics/btp352.
McMurdie, Paul J., and Susan Holmes. 2013. “Phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data.” PLOS ONE 8 (4): e61217. https://doi.org/10.1371/journal.pone.0061217.
Mölder, Felix, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall, Christopher H. Tomkins-Tinch, Vanessa Sochat, Jan Forster, et al. 2021. “Sustainable Data Analysis with Snakemake.” F1000Research 10 (April): 33. https://doi.org/10.12688/f1000research.29032.2.
Quast, Christian, Elmar Pruesse, Pelin Yilmaz, Jan Gerken, Timmy Schweer, Pablo Yarza, Jörg Peplies, and Frank Oliver Glöckner. 2013. “The SILVA Ribosomal RNA Gene Database Project: Improved Data Processing and Web-Based Tools.” Nucleic Acids Research 41 (D1): D590–96. https://doi.org/10.1093/nar/gks1219.
Schloss, Patrick D., Sarah L. Westcott, Thomas Ryabin, Justine R. Hall, Martin Hartmann, Emily B. Hollister, Ryan A. Lesniewski, et al. 2009. “Introducing Mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities.” Applied and Environmental Microbiology 75 (23): 7537–41. https://doi.org/10.1128/AEM.01541-09.
Wood, Derrick E., Jennifer Lu, and Ben Langmead. 2019. “Improved Metagenomic Analysis with Kraken 2.” Genome Biology 20 (1): 257. https://doi.org/10.1186/s13059-019-1891-0.