DADA2: High-resolution sample inference from Illumina amplicon data
Citations
8,821 citations
4,833 citations
2,475 citations
Cites background or methods from "DADA2: High-resolution sample infer..."
...Additionally, marker-gene amplicon sequence analysis pipelines commonly utilize denoising methods [4] to model per-run error profiles, filter noisy sequences, and resolve actual sequence variants....
[...]
...The exact sequences were used for cross validation and were not altered to simulate any sequencing error; thus, our benchmarks simulate denoised sequence data [4] and isolate classifier performance from impacts from sequencing errors....
[...]
...ngram_range [4,4], [8, 8], [16, 16], [4,16]...
[...]
...com/qiime2/q2-demux) and quality filtered and dereplicated with q2-dada2 [4]....
[...]
...Challenges in this process include the short length of typical sequencing reads with current technology, sequencing and PCR errors [4], selection of appropriate marker genes that contain sufficient heterogeneity to differentiate target species but that are homogeneous enough in some regions to design broad-spectrum primers, quality of reference sequence annotations [5], and selection of a method that accurately predicts the taxonomic affiliation of millions of sequences at low computational cost....
[...]
1,977 citations
1,287 citations
Cites background from "DADA2: High-resolution sample infer..."
...In marker-gene data, we expect the best performance will be achieved with post-denoising ASVs [53, 58] as ASVs are less prone than OTUs to grouping contaminants with related real strains....
[...]
References
28,911 citations
17,350 citations
11,904 citations
11,329 citations
8,410 citations