Go Back   SEQanswers > Literature Watch

Similar Threads
Thread Thread Starter Forum Replies Last Post
short reads from amplicon for 454 using Titanium chemistry pseudorabies 454 Pyrosequencing 9 08-15-2011 08:46 AM
amplicon preprocessing vs.shotgun processing litali 454 Pyrosequencing 4 02-16-2011 12:44 PM
Install spp (chip-seq processing pipeline) bbl Bioinformatics 0 10-27-2010 08:02 AM
PubMed: Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance Newsbot! Literature Watch 0 09-02-2010 03:00 AM
Mapping 454 reads using Galaxy online. Alex Clop Bioinformatics 1 08-12-2010 06:13 AM

Thread Tools
Old 09-20-2011, 03:00 AM   #1
RSS Posting Maniac

Join Date: Feb 2008
Posts: 1,443
Default PubMed: CLOTU: an online pipeline for processing and clustering of 454 amplicon reads

Syndicated from PubMed RSS Feeds

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

BMC Bioinformatics. 2011;12:182

Authors: Kumar S, Carlsen T, Mevik BH, Enger P, Blaalid R, Shalchian-Tabrizi K, Kauserud H

BACKGROUND: 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 (

PMID: 21599929 [PubMed - indexed for MEDLINE]

Newsbot! is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:11 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO