DADA2: High resolution sample inference from Illumina amplicon data repository
Abstract/Contents
- Abstract
- This is the repository accompanying the Nature Methods paper on DADA2. The repository contains the Extreme, Balanced and HMP data sets as well as five complete R markdown workflows and their html output. DADA2 is a software package that models and corrects Illumina- sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
Description
| Type of resource | software, multimedia |
|---|---|
| Date created | April 6, 2016 |
Creators/Contributors
| Author | Callahan, Benjamin J | |
|---|---|---|
| Author | McMurdie, Paul J | |
| Author | Rosen, Michael J | |
| Author | Han, Andrew W | |
| Author | Johnson, Amy Jo | |
| Author | Holmes, Susan P |
Subjects
| Subject | DADA2 |
|---|---|
| Subject | microbiome |
| Subject | probabilistic modeling |
| Subject | NGS |
| Subject | Illumina |
| Subject | amplicon |
| Subject | chimera |
| Genre | Dataset |
Bibliographic information
| Related Publication | Callahan, Benjamin J., et al. (2016). DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods. http://dx.doi.org/10.1038/nmeth.3869 |
|---|---|
| Location | https://purl.stanford.edu/mh194vj6733 |
Access conditions
- Use and reproduction
- User agrees that, where applicable, content will not be used to identify or to otherwise infringe the privacy or confidentiality rights of individuals. Content distributed via the Stanford Digital Repository may be subject to additional license and use restrictions applied by the depositor.
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
Preferred citation
- Preferred Citation
- Callahan, Benjamin J and McMurdie, Paul J and Rosen, Michael J and Han, Andrew W and Johnson, Amy Jo and Holmes, Susan P. (2016). DADA2: High resolution sample inference from Illumina amplicon data repository. Stanford Digital Repository. Available at: http://purl.stanford.edu/mh194vj6733
Collection
Reproducible Research Support for Statistics of the Microbiome
View other items in this collection in SearchWorksContact information
- Contact
- susan@stat.stanford.edu
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