Unless otherwise stated, UCHIME results were obtained using the USEARCH v4.2.52. Perseus results were obtained using v1.24 of the AmpliconNoise package. MAFFT v6.853 (Katoh and Toh, 2008 (link)) was used by Perseus to create alignments. The reference database used for both ChimeraSlayer and UCHIME was the ‘gold’ set in http://sourceforge.net/projects/microbiomeutil/files/ , version 2011-11-02. Unless otherwise stated, Perseus results were obtained using PerseusD v1.24, a variant of the original Perseus algorithm that follows UCHIME by only testing parents that have been classified as non-chimeric and are at least twice as abundant as the query. For a comparison of Perseus with PerseusD, see the Supplemental Material.
Protocol detail
Chimera Detection in Amplicon Sequencing
Partial Protocol Preview
This section provides a glimpse into the protocol.
The remaining content is hidden due to licensing restrictions, but the full text is available at the following link:
Access Free Full Text.
Corresponding Organization :
Other organizations : Broad Institute, University of Colorado Boulder, University of Glasgow
Top 5 similar protocols
Protocol cited in 2 377 other protocols
Variable analysis
independent variables
- UCHIME results obtained using the USEARCH v4.2.52
- Perseus results obtained using v1.24 of the AmpliconNoise package
- MAFFT v6.853 used by Perseus to create alignments
- Reference database used for both ChimeraSlayer and UCHIME was the 'gold' set in http://sourceforge.net/projects/microbiomeutil/files/, version 2011-11-02
- Perseus results obtained using PerseusD v1.24, a variant of the original Perseus algorithm that follows UCHIME by only testing parents that have been classified as non-chimeric and are at least twice as abundant as the query
- Not explicitly mentioned
- Not explicitly mentioned
- Not mentioned
- Not mentioned
Annotations
Based on most similar protocols
Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.
Sign up for free or login to display all annotations
As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!