Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution

By Jens Reeder, Rob Knight. Nature Methods, 2010

702 citations recorded by the source corpus.

We developed a fast method for denoising pyrosequencing for community 16S rRNA analysis. We observe a 2–4 fold reduction in the number of observed OTUs (operational taxonomic units) comparing denoised with non-denoised data. ~50,000 sequences can be denoised on a laptop within an hour, two orders of magnitude faster than published techniques. We demonstrate the effects of denoising on alpha and beta diversity of large 16S rRNA datasets.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/05cd3c85614da3ce15935404328bfda0826de48c

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Citations in the corpus

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses (2013, methodology): “851 [19], and chimeric sequences were detected using UCHIME [20] and deleted.”
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies (2011, methodology): “The third approach was the development of two denoising algorithms, PyroNoise and DeNoiser, which correct the base calls by modeling the original flowgram data [23–25]; unfortunately, these methods have received limited application because they require high computational resources and have had imple”
Conducting a Microbiome Study (2014, methodology): “Denoising was developed for reducing sequencing errors on the 454 platform and does not apply to Illumina data (Reeder and Knight, 2010).”
Active and total microbial communities in forest soil are largely different and highly stratified during decomposition (2011, methodology): “851 (Reeder and Knight, 2010) and chimeric sequences were detected using UCHIME (Edgar, 2010) and deleted.”
Fungal community on decomposing leaf litter undergoes rapid successional changes (2012, methodology): “851 (Reeder and Knight, 2010) and chimeric sequences were detected using UCHIME (Edgar, 2010) and deleted.”
Advancing our understanding of the human microbiome using QIIME (2013, methodology): “However, to successfully remove the read artifacts, a denoising process has to be performed (Reeder & Knight, 2010) to reduce the impact of homopolymer runs (runs of the same base).”
Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide (2013, methodology): “The read-score-based base-pair pruning applied by the sequencing factory is at best a poor replacement for sequence quality management programs such as AMPLICONNOISE (Quince et al., 2011), the Denoiser implemented in QIIME (Reeder & Knight, 2010), DADA (Rosen et al., 2012) and ACACIA (Bragg et al., ”
A Selected Core Microbiome Drives the Early Stages of Three Popular Italian Cheese Manufactures (2014, methodology): “For 16S rRNA gene reads, the analysis was carried out as follows: sequences that passed the quality filter were denoised [26] and singletons were excluded.”
Removing Noise From Pyrosequenced Amplicons (2011, methodology): “However, the results here suggest that both agglomerative approaches must be treated with caution, by not simply looking at OTU numbers as in previous evaluations [9,10], but rather their identity we have established that these are prone to over-clustering, removing a substantial fraction of the tru”
Bacillus asahii comes to the fore in organic manure fertilized alkaline soils (2015, methodology): “Sequences were denoised 159 (Reeder and Knight, 2010) and then binned into operational taxonomic units (OTUs) 160 using a 97% identity threshold, and the most abundant sequence from each OTU was 161 8 selected as a representative sequence for that OTU.”
Similar community assembly mechanisms underlie similar biogeography of rare and abundant bacteria in lakes on Yungui Plateau, China (2017, methodology): “To further improve quality, resulting sequences were denoised using DeNoiser version 0.851 (Reeder and Knight 2010) and putative chimeras were detected and excluded with UCHIME (Edgar et al. 2011).”
Independent roles of ectomycorrhizal and saprotrophic communities in soil organic matter decomposition (2013, methodology): “To account for sequencing error that can arise as part of the PCR and 454 sequencing process, we used flowgram clustering (Reeder and Knight, 2010) implemented in the denoise_wrapper.py command using a Titanium error profile.”
Error filtering, pair assembly and error correction for next-generation sequencing reads (2015, methodology): “, 2011) and an unnamed method (Reeder and Knight, 2010) that uses a greedy algorithm based on an abundance sort.”