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NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads

Mohamed Mysara, Natalie Leys, Jeroen Raes, Pieter Monsieurs
2015 BMC Bioinformatics  
Conclusions: NoDe was shown to be a computational efficient denoising algorithm for pyrosequencing reads, producing the lowest error rates in an extensive benchmarking study with other denoising algorithms  ...  clusters those error-prone reads with correct reads resulting in error-free representative read.  ...  Acknowledgements The authors would like to thank Patrick Schloss for supplying us with the chimera prediction of the MOCK1 data.  ... 
doi:10.1186/s12859-015-0520-5 pmid:25888405 pmcid:PMC4403973 fatcat:ukhric3dfnhita3psj7aaaphba

Efficient error correction for next-generation sequencing of viral amplicons

Pavel Skums, Zoya Dimitrova, David S Campo, Gilberto Vaughan, Livia Rossi, Joseph C Forbi, Jonny Yokosawa, Alex Zelikovsky, Yury Khudyakov
2012 BMC Bioinformatics  
Results: In this paper, we present two new efficient error correction algorithms optimized for viral amplicons: (i) k-mer-based error correction (KEC) and (ii) empirical frequency threshold (ET).  ...  All these parameters are strongly sequence specific and should be incorporated into the calibration of error-correction algorithms designed for amplicon sequencing.  ...  We thank the Biotechnology Core Facility (Centers for Disease Control and Prevention) for successfully running our samples on the 454/Roche GS FLX instrument. Author details  ... 
doi:10.1186/1471-2105-13-s10-s6 pmid:22759430 pmcid:PMC3382444 fatcat:jm6sbyq5kneihixf3ib73z32n4

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

Z. Liu, T. Z. DeSantis, G. L. Andersen, R. Knight
2008 Nucleic Acids Research  
However, a major challenge is to design a workflow so that taxonomic information can be accurately and rapidly assigned to each read, so that the composition of each community can be linked back to likely  ...  Here, we use three large 16S rRNA datasets to test whether taxonomic information based on the full-length sequences can be recaptured by short reads that simulate the pyrosequencer outputs.  ...  Gordon for critical discussion of the article. We thank J. K. Harris, J. J. Walker and N. R. Pace for sharing unpublished data.  ... 
doi:10.1093/nar/gkn491 pmid:18723574 pmcid:PMC2566877 fatcat:gso7ddntdrfmhp5az45olxzvn4

Insights into functional bacterial diversity and its effects on Alpine bog ecosystem functioning

Anastasia Bragina, Christian Berg, Henry Müller, Daniel Moser, Gabriele Berg
2013 Scientific Reports  
A high abundance and diversity of nitrogenase genes were detected, mostly specific for each Sphagnum.  ...  for the climate-relevant ecosystem itself.  ...  Acknowledgements We are grateful to Benli Chai (East Lansing) for excellent cooperation using and improving the FunGene Pipeline and Stefan Lackner (Graz) for helpful discussions on network analysis.  ... 
doi:10.1038/srep01955 pmid:23739741 fatcat:mljvo6nhmjdgjd3qt3w6utmkwm

Environmental bio-monitoring with high-throughput sequencing

J. Wang, P. A. McLenachan, P. J. Biggs, L. H. Winder, B. I. K. Schoenfeld, V. V. Narayan, B. J. Phiri, P. J. Lockhart
2013 Briefings in Bioinformatics  
Educators can help by nurturing a collaborative interdisciplinary approach to genome science, which is essential for effective problem solving.  ...  However, there are experimental and analytical issues to consider before applying a sequencing technology, which was originally developed for genome projects, to ecological projects.  ...  A low yield of DNA has been a problem for highthroughput sequencing protocols-pyrosequencing and some Illumina protocols require microgram amounts for DNA library construction.  ... 
doi:10.1093/bib/bbt032 pmid:23677899 fatcat:636pjwjsfbd5nlflraw3qflprm

Insights into the distribution and abundance of the ubiquitous Candidatus Saccharibacteria phylum following tag pyrosequencing

Belinda Ferrari, Tristrom Winsley, Mukan Ji, Brett Neilan
2014 Scientific Reports  
Here, the application of two taxon-specific primers on environmental and human-associated samples using bar-coded tag pyrosequencing revealed two new clades for this phylum to exist and we propose that  ...  as a host of clinical environments.  ...  We would also like to thank researchers from UNSW, Macquarie University and the Australian Antarctic Division for the supply of gDNA from a range of samples; Drs Nathan Fenning for the supply of clinical  ... 
doi:10.1038/srep03957 pmid:24492458 pmcid:PMC5379237 fatcat:l7m4wcuggfeh3eneep5qb5d3oq

Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA

Jon Bråte, Ramiro Logares, Cédric Berney, Dan Kristofer Ree, Dag Klaveness, Kjetill S Jakobsen, Kamran Shalchian-Tabrizi
2010 The ISME Journal  
Thus, our new strategy for 454 amplicon sequencing was able to recover a large diversity of distantly related eukaryotes and previously unknown species of Perkinsea.  ...  Our approach included 454 pyrosequencing of the 18S rDNA gene obtained from a high-altitude lake (Lake Finsevatn, Norway) and phylogenetic analyses of all publicly available sequences related to Perkinsea  ...  Acknowledgements We thank the Bioportal team for implementing bioinformatics applications on the Bioportal (http://www.  ... 
doi:10.1038/ismej.2010.39 pmid:20393574 fatcat:upe2gzzxyzar5pp7ulrrnge4y4

Accuracy of protist diversity assessments: morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study

Charles Bachy, John R Dolan, Purificación López-García, Philippe Deschamps, David Moreira
2012 The ISME Journal  
transcribed spacer (ITS) regions, applying a variety of computational approaches currently used to analyze pyrosequence reads.  ...  The 18S ribosomal DNA (rDNA) pyrosequencing has revealed a vast diversity of infrequent sequences, leading to the proposition of the existence of an extremely diverse microbial 'rare biosphere'.  ...  We thank two anonymous referees for their useful suggestions.  ... 
doi:10.1038/ismej.2012.106 pmid:23038176 pmcid:PMC3554406 fatcat:aerau7xnljdnhokiast5gaflze

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

J. R. Cole, Q. Wang, E. Cardenas, J. Fish, B. Chai, R. J. Farris, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, T. Marsh, G. M. Garrity, J. M. Tiedje
2009 Nucleic Acids Research  
It provides a much more intuitive handling of sequencing errors.  ...  In addition, a new Taxomatic visualization tool allows rapid visualization of taxonomic inconsistencies and suggests corrections, and a new class Assignment Generator provides instructors with a lesson  ...  A typical pyrosequencing run of 350 000 reads requires about 10 CPU-minutes for the initial processing steps with a 2.66 GHz processor.  ... 
doi:10.1093/nar/gkn879 pmid:19004872 pmcid:PMC2686447 fatcat:6alemccr6bezhfixwcnc5n2cxe

CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction

Florent E Angly, Paul G Dennis, Adam Skarshewski, Inka Vanwonterghem, Philip Hugenholtz, Gene W Tyson
2014 Microbiome  
Copyrighter is a new tool for gene copy number bias correction GCN varies by over an order of magnitude between microbial species and, thus, a one-to-one relationship between a 16S rRNA gene amplicon read  ...  The 16S rRNA gene amplicon reads (deposited under accession number SRR1145444) were processed using the bioinformatic pipeline described above, using 800 reads for the rarefaction step, and corrected for  ...  Corrected profiles with a significantly lower distance than the corresponding uncorrected profiles (unilateral exact Mann-Whitney test, P < 0.05) are marked with a star.  ... 
doi:10.1186/2049-2618-2-11 pmid:24708850 pmcid:PMC4021573 fatcat:qkdmwonhrndiniu3sbsh3ca7te

Bioinformatics tools and databases for analysis of next-generation sequence data

H. C. Lee, K. Lai, M. T. Lorenc, M. Imelfort, C. Duran, D. Edwards
2011 Briefings in Functional Genomics  
Here, we outline some of the tools and databases commonly used for the analysis of next-generation sequence data with comment on their utility.  ...  With data production now no longer being limited, there is a huge challenge to analyse the data flood and interpret biological meaning.  ...  C.D. is a PhD student under the supervision of D.E. and is currently employed as a bioinformatics software developer by Biomatters Ltd.  ... 
doi:10.1093/bfgp/elr037 pmid:22184335 fatcat:7lphlq4uivhcxpsndhzgv5uhpq

Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics

Seth M. Bybee, Heather Bracken-Grissom, Benjamin D. Haynes, Russell A. Hermansen, Robert L. Byers, Mark J. Clement, Joshua A. Udall, Edward R. Wilcox, Keith A. Crandall
2011 Genome Biology and Evolution  
Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on nextgen capacity to sequence large numbers of targeted gene regions from a large number of samples.  ...  Our TAS approach includes a bioinformatic application, BarcodeCrucher, to take raw next-gen sequence reads and perform quality control checks and convert the data into FASTA format organized by gene and  ...  We thank our collaborators, many of whom have been working with us for 15 years, for samples, advice, and comments. We thank two anonymous reviewers for helpful comments to improve our manuscript.  ... 
doi:10.1093/gbe/evr106 pmid:22002916 pmcid:PMC3236605 fatcat:nm2vp77morgcviymixjga3oy5i

Next-generation sequencing reveals large connected networks of intra-host HCV variants

David S Campo, Zoya Dimitrova, Lilian Yamasaki, Pavel Skums, Daryl TY Lau, Gilberto Vaughan, Joseph C Forbi, Chong-Gee Teo, Yury Khudyakov
2014 BMC Genomics  
After NGS error correction, the average number of reads and variants obtained from each sample were 3202 and 464, respectively.  ...  The work focused on large components having > 5% of all reads, which in average account for 93.7% of all reads found in a patient.  ...  After NGS sequencing error correction, the average number of reads and variants obtained from each sample were 3202.43 (Standard Error of the Mean, S.E.M. = 330.41) and 464 (S.E.M. = 79.98), respectively  ... 
doi:10.1186/1471-2164-15-s5-s4 pmid:25081811 pmcid:PMC4120142 fatcat:h564ucldjrebrew2ua7krfc5ny

Robust Computational Analysis of rRNA Hypervariable Tag Datasets

Maksim Sipos, Patricio Jeraldo, Nicholas Chia, Ani Qu, A. Singh Dhillon, Michael E. Konkel, Karen E. Nelson, Bryan A. White, Nigel Goldenfeld, Art F. Y. Poon
2010 PLoS ONE  
We introduce two metrics to ascertain the quality of clustering of pyrosequenced rRNA data, and show that complete linkage clustering greatly outperforms other widely used methods.  ...  The fragmented nature of the 16S rRNA datasets obtained, coupled with their unprecedented size, has led to the recognition that the results of such analyses are potentially contaminated by a variety of  ...  Acknowledgments We thank Dennis Schaberg for assistance with the inoculation of the chickens with C. jejuni and Stuart Perry for animal care.  ... 
doi:10.1371/journal.pone.0015220 pmid:21217830 pmcid:PMC3013109 fatcat:zeqji5hpj5e7vmha6da2u2vnzi

FunGene: the functional gene pipeline and repository

Jordan A. Fish, Benli Chai, Qiong Wang, Yanni Sun, C. Titus Brown, James M. Tiedje, James R. Cole
2013 Frontiers in Microbiology  
For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence.  ...  Additional FunGene tools are specialized to process coding gene amplicon data.  ...  The algorithm takes as input a sorted list of thin edges; our implementation computes and sorts the distances on disk using either a single threaded algorithm, or a Hadoop (v0.18) map-reduce algorithm.  ... 
doi:10.3389/fmicb.2013.00291 pmid:24101916 pmcid:PMC3787254 fatcat:gacyurs27rfmzmiupxjgbrmisy
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