CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation.

Background The implementation of high throughput sequence analyses for exploring biodiversity sets high demands for bioinformatics applications for automated data processing. Here we introduce CLOTU, which is 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 single reads and run BLAST against NCBInr or a customized database in a super-computing environment. The resulting data is browsed in a user-friendly manner, easy to forward to further downstream analyses. Although CLOTU is especially designed for analyzing 454 amplicon reads, other types of DNA sequence data can also be analyzed. 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).