Kelpie: generating full-length ‘amplicons’ from whole-metagenome datasets

The Coal Seam Microbiome (CSMB) reference set, a lingua franca for the microbial coal-to-methane community

(2018) Silas H.W. Vick et al.   INTERNATIONAL JOURNAL OF COAL GEOLOGY

Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling

(2018) Garold Fuks et al.   Microbiome

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies

(2017) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

(2017) Tobias Guldberg Frøslev et al.   Nature Communications

An evaluation of the accuracy and speed of metagenome analysis tools

(2016) Stinus Lindgreen et al.   Scientific Reports

Tag jumps illuminated - reducing sequence-to-sample misidentifications in metabarcoding studies

(2015) Ida Baerholm Schnell et al.   Molecular Ecology Resources

Xander: employing a novel method for efficient gene-targeted metagenomic assembly

(2015) Qiong Wang et al.   Microbiome

Blue: correcting sequencing errors using consensus and context

(2014) Paul Greenfield et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Answering biological questions by querying k-mer databases

(2012) Paul Greenfield et al.   CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

(2011) Christopher S Miller et al.   GENOME BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Insidious effects of sequencing errors on perceived diversity in molecular surveys

(2010) Ian A. Dickie   NEW PHYTOLOGIST