BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

Evolution of microsporidia: An extremely successful group of eukaryotic intracellular parasites

(2020) Lina Wadi et al.   PLoS Pathogens

MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics

(2020) Eli Levy Karin et al.   Microbiome

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

OrthoDB in 2020: evolutionary and functional annotations of orthologs

(2020) Evgeny M Zdobnov et al.   NUCLEIC ACIDS RESEARCH

Bioconda: sustainable and comprehensive software distribution for the life sciences

(2018) Björn Grüning et al.   NATURE METHODS

OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs

(2018) Evgenia V Kriventseva et al.   NUCLEIC ACIDS RESEARCH

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

NCBI Viral Genomes Resource

(2014) J. Rodney Brister et al.   NUCLEIC ACIDS RESEARCH

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS