Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 4,401

The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

Open access
Bokulich, Nicholas A, Subramanian, Sathish, Faith, Jeremiah J, Gevers, Dirk, Gordon, Jeffrey I, Knight, Rob, Mills, David A, Caporaso, J Gregory·2013·Nature Methods
DOI 10.1038/nmeth.2276
Open this paper in CoChat — free account

Abstract

High-throughput sequencing has revolutionized microbial ecology, but read quality remains a considerable barrier to accurate taxonomy assignment and α-diversity assessment for microbial communities. We demonstrate that high-quality read length and abundance are the primary factors differentiating correct from erroneous reads produced by Illumina GAIIx, HiSeq and MiSeq instruments. We present guidelines for user-defined quality-filtering strategies, enabling efficient extraction of high-quality data and facilitating interpretation of Illumina sequencing results.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/nmeth.2276

Cites

4 of 4 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 4 references

Research works printed but not linked: 11

  1. Gilbert, J.A. & Meyer, F. ASM Microbe 7, 64–69 (2012).
  2. Reeder, J. & Knight, R. Nat. Methods 7, 668–669 (2010). · DOI · Paper page
  3. Quince, C. et al. Nat. Methods 6, 639–641 (2009). · DOI
  4. Caporaso, J.G. et al. Proc. Natl. Acad. Sci. USA 108, 4516–4522 (2011). · DOI · Paper page
  5. Minoche, A.E. et al. Genome Biol. 12, R112 (2011). · DOI · Paper page
  6. Caporaso, J.G. et al. ISME J. 6, 1621–1624 (2012). · DOI · Paper page
  7. Bokulich, N.A. et al. PLoS ONE 7, e36357 (2012). · DOI
  8. Bokulich, N.A., Bamforth, C.W. & Mills, D.A. PLoS ONE 7, e35507 (2012). · DOI
  9. Edgar, R.C. Bioinformatics 26, 2460–2461 (2010). · DOI · Paper page
  10. Wang, Q., Garrity, G.M., Tiedje, J.M. & Cole, J.R. Appl. Environ. Microbiol. 73, 5261–5267 (2007). · DOI · Paper page
  11. Caporaso, J.G. et al. Bioinformatics 26, 266–267 (2010). · DOI · Paper page

Cited by

Metadata

Authors
Bokulich, N. A., Subramanian, S., Faith, J. J., Gevers, D., Gordon, J. I., Knight, R., Mills, D. A., & Caporaso, J. G.
Venue
Nature Methods
Publisher
Springer Science and Business Media LLC
Published
2013-01
Volume
10
Issue
1
Pages
57-59
ISSN
  • 1548-7091 (ISSN-L)
  • 1548-7105
DOI
10.1038/nmeth.2276
OpenAlex
W2086865963
Cited by
4,401
References
4
FWCI
17.54
Type
journal article
Language
en
Open access
green
Licence
www.springer.com/tdm (tdm)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.