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dc.date.accessioned2013-04-18T10:24:48Z
dc.date.available2013-04-18T10:24:48Z
dc.date.issued2011en_US
dc.date.submitted2011-07-06en_US
dc.identifier.citationKumar, Surendra, Carlsen, Tor, Mevik, Bjørn-Helge, Enger, Pål, Blaalid, Rakel, Shalchian-Tabrizi, Kamran, Kauserud, Håvard. CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation. BMC Bioinformaticsen_US
dc.identifier.urihttp://hdl.handle.net/10852/11573
dc.description.abstractBackground:The implementation of high throughput sequencing for exploring biodiversity poses high demands on bioinformatics applications for automated data processing. Here we introduce CLOTU, an online and open access pipeline for processing 454 amplicon reads. CLOTU has been constructed to be highly user-friendly and flexible, since different types of analyses are needed for different datasets. Results:In CLOTU, the user can filter out low quality sequences, trim tags, primers, adaptors, perform clustering of sequence reads, and run BLAST against NCBInr or a customized database in a high performance computing environment. The resulting data may be browsed in a user-friendly manner and easily forwarded to downstream analyses. Although CLOTU is specifically designed for analyzing 454 amplicon reads, other types of DNA sequence data can also be processed. A fungal ITS sequence dataset generated by 454 sequencing of environmental samples is used to demonstrate the utility of CLOTU. Conclusions:CLOTU is a flexible and easy to use bioinformatics pipeline that includes different options for filtering, trimming, clustering and taxonomic annotation of high throughput sequence reads. Some of these options are not included in comparable pipelines. CLOTU is implemented in a Linux computer cluster and is freely accessible to academic users through the Bioportal web-based bioinformatics service (http://www.bioportal.uio.no).eng
dc.language.isoengen_US
dc.rightsAttribution 2.0 Generic
dc.rights.urihttp://creativecommons.org/licenses/by/2.0/
dc.titleCLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotationen_US
dc.typeJournal articleen_US
dc.date.updated2013-04-15en_US
dc.creator.authorKumar, Surendraen_US
dc.creator.authorCarlsen, Toren_US
dc.creator.authorMevik, Bjørn-Helgeen_US
dc.creator.authorEnger, Pålen_US
dc.creator.authorBlaalid, Rakelen_US
dc.creator.authorShalchian-Tabrizi, Kamranen_US
dc.creator.authorKauserud, Håvarden_US
dc.subject.nsiVDP::470en_US
cristin.unitcode152100en_US
cristin.unitnameBiologisk institutten_US
dc.identifier.cristin805562en_US
dc.identifier.bibliographiccitationinfo:ofi/fmt:kev:mtx:ctx&ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=BMC Bioinformatics&rft.volume=12en_US
dc.identifier.jtitleBMC Bioinformatics
dc.identifier.volume12
dc.identifier.doihttp://dx.doi.org/10.1186/1471-2105-12-182
dc.identifier.urnURN:NBN:no-28926en_US
dc.type.documentTidsskriftartikkelen_US
dc.identifier.duo131967en_US
dc.type.peerreviewedPeer revieweden_US
dc.identifier.fulltextFulltext https://www.duo.uio.no/bitstream/handle/10852/11573/1/CLOTU.pdf
dc.type.versionPublishedVersion
cristin.articleid182


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