• Publications
  • Influence
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
  • R. Edgar
  • Biology, Medicine
  • Nucleic acids research
  • 1 March 2004
TLDR
MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning. Expand
Search and clustering orders of magnitude faster than BLAST
  • R. Edgar
  • Medicine, Computer Science
  • Bioinform.
  • 1 October 2010
TLDR
UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets. Expand
UPARSE: highly accurate OTU sequences from microbial amplicon reads
  • R. Edgar
  • Biology, Medicine
  • Nature Methods
  • 1 October 2013
TLDR
The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% correct bases commonly reported by other methods. Expand
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
  • R. Edgar
  • Computer Science, Medicine
  • BMC Bioinformatics
  • 19 August 2004
TLDR
MUSCLE offers a range of options that provide improved speed and / or alignment accuracy compared with currently available programs, and a new option, MUSCLE-fast, designed for high-throughput applications. Expand
UCHIME improves sensitivity and speed of chimera detection
TLDR
UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences, and in testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. Expand
Structure, Function and Diversity of the Healthy Human Microbiome
TLDR
The Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far, finding the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. Expand
Defining the core Arabidopsis thaliana root microbiome
TLDR
The pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants is reported to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages. Expand
Error filtering, pair assembly and error correction for next-generation sequencing reads
TLDR
This work demonstrates large reductions in error frequencies, especially for high-error-rate reads, by three independent means: filtering reads according to their expected number of errors, assembling overlapping read pairs and by exploiting unique sequence abundances to perform error correction. Expand
UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing
TLDR
UNOISE2 is described, an updated version of the UNOISE algorithm for denoising (error-correcting) Illumina amplicon reads and it is shown that it has comparable or better accuracy than DADA2. Expand
SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS sequences
TLDR
The SINTAX algorithm predicts taxonomy by using k-mer similarity to identify the top hit in a reference database and provides bootstrap confidence for all ranks in the prediction, achieving comparable or better accuracy to the RDP Naive Bayesian Classifier with a simpler algorithm that does not require training. Expand
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