Cutadapt removes adapter sequences from high-throughput sequencing reads

By Marcel Martin. 2011

31,177 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/17d01d94092942d99625e2df0614a03977f64960

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In Molecular Biology

Citations in the corpus

The “Plastisphere” of Biodegradable Plastics Is Characterized by Specific Microbial Taxa of Alpine and Arctic Soils (2020, methodology): “PCR primers were removed using Cutadapt (Martin, 2011) allowing for a maximum of one mismatch in the forward and reverse primer.”
ipyrad: Interactive assembly and analysis of RADseq datasets (2020, methodology): “…written in Python, it retains high performance through the use of just-in-time compilation (Lam et al., 2015), and incorporation of industry standard compiled software into the assembly pipeline (Edgar, 2004; Li et al., 2009; Li and Durbin, 2009; Martin, 2011; Quinlan, 2014; Rognes et al., 2016).”
Evidence that the endometrial microbiota has an effect on implantation success or failure. (2016, background): “The vaginal microbiota typically changes throughout themenstrual cycle, dependingon factors such as vaginal hygiene, sexual activity, use of intimate products, and underwear composition; greater microbiota stability is associated with the estradiol peak at ovulation and progesterone rise in the midl”
Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates (2017, methodology): “Tag and primer sequences were trimmed with CUTADAPT 34 .”
Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming (2018, methodology): “Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads.”
Comparison of Sequencing Utility Programs (2013, methodology): “Two of these techniques, adapter clipping and paired-end joining are discussed.”
Melanization of mycorrhizal fungal necromass structures microbial decomposer communities (2018, methodology): “Briefly, primers were trimmed using cutadapt (Martin, 2011), forward and reverse reads were paired using PEAR (Zhang, Kobert, Flouri, & Stamatakis, 2013), and the SSU and 5.”
Global Mapping of Small RNA-Target Interactions in Bacteria (2016, methodology): “The paired reads were then processed by cutadapt (Martin, 2011)”
Temperatures beyond the community optimum promote the dominance of heat-adapted, fast growing and stress resistant bacteria in alpine soils (2020, methodology): “PCR primers were removed using Cutadapt (Martin, 2011) allowing for a maximum of one mismatch in the forward and reverse primer.”