Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
Recent advances have made it possible to analyze high-throughput marker-gene
sequencing data without resorting to the customary construction of molecular operational …
sequencing data without resorting to the customary construction of molecular operational …
[HTML][HTML] Environmental DNA–An emerging tool in conservation for monitoring past and present biodiversity
PF Thomsen, E Willerslev - Biological conservation, 2015 - Elsevier
The continuous decline in Earth's biodiversity represents a major crisis and challenge for the
21st century, and there is international political agreement to slow down or halt this decline …
21st century, and there is international political agreement to slow down or halt this decline …
Patterns in soil microbial diversity across Europe
Factors driving microbial community composition and diversity are well established but the
relationship with microbial functioning is poorly understood, especially at large scales. We …
relationship with microbial functioning is poorly understood, especially at large scales. We …
Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity
Despite advances in sequencing, lack of standardization makes comparisons across studies
challenging and hampers insights into the structure and function of microbial communities …
challenging and hampers insights into the structure and function of microbial communities …
Deblur rapidly resolves single-nucleotide community sequence patterns
High-throughput sequencing of 16S ribosomal RNA gene amplicons has facilitated
understanding of complex microbial communities, but the inherent noise in PCR and DNA …
understanding of complex microbial communities, but the inherent noise in PCR and DNA …
UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing
RC Edgar - BioRxiv, 2016 - biorxiv.org
Amplicon sequencing of tags such as 16S and ITS ribosomal RNA is a popular method for
investigating microbial populations. In such experiments, sequence errors caused by PCR …
investigating microbial populations. In such experiments, sequence errors caused by PCR …
Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples
AE Parada, DM Needham… - Environmental …, 2016 - Wiley Online Library
Microbial community analysis via high‐throughput sequencing of amplified 16S rRNA genes
is an essential microbiology tool. We found the popular primer pair 515F (515F‐C) and …
is an essential microbiology tool. We found the popular primer pair 515F (515F‐C) and …
DADA2: High-resolution sample inference from Illumina amplicon data
We present the open-source software package DADA2 for modeling and correcting Illumina-
sequenced amplicon errors (https://github. com/benjjneb/dada2). DADA2 infers sample …
sequenced amplicon errors (https://github. com/benjjneb/dada2). DADA2 infers sample …
Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment
Effective marine management requires comprehensive data on the status of marine
biodiversity. However, efficient methods that can document biodiversity in our oceans are …
biodiversity. However, efficient methods that can document biodiversity in our oceans are …
Error filtering, pair assembly and error correction for next-generation sequencing reads
RC Edgar, H Flyvbjerg - Bioinformatics, 2015 - academic.oup.com
Motivation: Next-generation sequencing produces vast amounts of data with errors that are
difficult to distinguish from true biological variation when coverage is low. Results: We …
difficult to distinguish from true biological variation when coverage is low. Results: We …