DECIPHER, a Search-Based Approach to Chimera Identification for 16S rRNA Sequences

By Erik S. Wright, L. Ş. Yilmaz, Daniel R. Noguera. Applied and Environmental Microbiology, 2011

661 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/2bd115a0b334a4f9e47bd738af006f8958310687

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

In Molecular Biology

Citations in the corpus

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi (2015, neutral): “DECIPHER (Wright et al. 2012) (http://decipher.cee.wisc. edu/index.html) for bacterial 16S sequences searches for sets of short fragments that are uncommon in the phylogenetic group where the sequence is classified, but frequent in other phylogenetic groups.”
Soil microbial community under a nurse-plant species changes in composition, biomass and activity as the nurse grows (2013, methodology): “Chimeras were identified using Decipher’s Find chimeras tool (Wright et al., 2011) and removed from the dataset.”
obitools: a unix‐inspired software package for DNA metabarcoding (2016, background): “This latter category can be identiﬁed using dedicated programs (e.g. Edgar et al. 2011; Quince et al. 2011; Wright et al. 2012).”
DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment (2015, background): “Furthermore, real sequence sets often include spurious (e.g., chimeric [16]) sequences, sequencing errors, uneven taxon sampling, rearrangements, and uneven lengths that have largely been neglected in studies relying on simulations.”
Conducting a Microbiome Study (2014, methodology): “There are several software options for chimera filtering, including ChimeraSlayer (Haas et al., 2011), UCHIME (Edgar et al., 2011), DECIPHER (Wright et al., 2012), and Perseus (Quince et al., 2011).”
Interactions among soil, plants, and microorganisms drive secondary succession in a dry environment (2014, methodology): “Chimeras were identified using Decipher's Find chimeras tool (Wright et al., 2012) and removed from the dataset.”