WGSQuikr: Fast Whole-Genome Shotgun Metagenomic Classification Public Deposited

http://ir.library.oregonstate.edu/concern/articles/r207tr112

This is the publisher’s final pdf. © 2014 Koslicki et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The published article can be found at:  http://www.plosone.org/home.action. At the author's request, we have also posted the author's accepted manuscript version.

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  • With the decrease in cost and increase in output of whole-genome shotgun technologies, many metagenomic studies are utilizing this approach in lieu of the more traditional 16S rRNA amplicon technique. Due to the large number of relatively short reads output from whole-genome shotgun technologies, there is a need for fast and accurate short-read OTU classifiers. While there are relatively fast and accurate algorithms available, such as MetaPhlAn, MetaPhyler, PhyloPythiaS, and PhymmBL, these algorithms still classify samples in a read-by-read fashion and so execution times can range from hours to days on large datasets. We introduce WGSQuikr, a reconstruction method which can compute a vector of taxonomic assignments and their proportions in the sample with remarkable speed and accuracy. We demonstrate on simulated data that WGSQuikr is typically more accurate and up to an order of magnitude faster than the aforementioned classification algorithms. We also verify the utility of WGSQuikr on real biological data in the form of a mock community. WGSQuikr is a Whole-Genome Shotgun QUadratic, Iterative, K-mer based Reconstruction method which extends the previously introduced 16S rRNA-based algorithm Quikr. A MATLAB implementation of WGSQuikr is available at: http://sourceforge.net/ projects/wgsquikr.
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  • Koslicki D, Foucart S, Rosen G (2014) WGSQuikr: Fast Whole-Genome Shotgun Metagenomic Classification. PLoS ONE 9(3): e91784. doi:10.1371/journal. pone.0091784
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  • description.provenance : Submitted by Deanne Bruner (deanne.bruner@oregonstate.edu) on 2014-05-07T23:16:41Z No. of bitstreams: 3 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) KoslickiDavidMathematicsWGSQuikrFastWhole.pdf: 745960 bytes, checksum: 58e6915743ce652a087822cacb51b9e3 (MD5) KoslickiDavidMathematicsWGSQuikrFastWhole(AcceptedManuscript).pdf: 195735 bytes, checksum: e4ee56273980190be8af9a1eb523ab8d (MD5)
  • description.provenance : Approved for entry into archive by Deanne Bruner(deanne.bruner@oregonstate.edu) on 2014-05-07T23:18:52Z (GMT) No. of bitstreams: 3 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) KoslickiDavidMathematicsWGSQuikrFastWhole.pdf: 745960 bytes, checksum: 58e6915743ce652a087822cacb51b9e3 (MD5) KoslickiDavidMathematicsWGSQuikrFastWhole(AcceptedManuscript).pdf: 195735 bytes, checksum: e4ee56273980190be8af9a1eb523ab8d (MD5)
  • description.provenance : Made available in DSpace on 2014-05-07T23:18:52Z (GMT). No. of bitstreams: 3 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) KoslickiDavidMathematicsWGSQuikrFastWhole.pdf: 745960 bytes, checksum: 58e6915743ce652a087822cacb51b9e3 (MD5) KoslickiDavidMathematicsWGSQuikrFastWhole(AcceptedManuscript).pdf: 195735 bytes, checksum: e4ee56273980190be8af9a1eb523ab8d (MD5) Previous issue date: 2014-03-13

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