Virome and metagenomic sequencing reveal the impact of microbial inoculants on suppressions of antibiotic resistome and viruses during co-composting

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony Bolger, Marc Lohse, Björn Usadel · Bioinformatics · 2014 · 69.7K citations · Full text

Life Sciences, Bioinformatics, Molecular Biology +13

Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, Richard Durbin · Bioinformatics · 2009 · 62.8K citations · Full text

Life Sciences, Bioinformatics, Biology +12

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

Stephen Nayfach, Antônio Pedro Camargo, Frederik Schulz et al. · Nature Biotechnology · 2020 · 1.8K citations · Full text

Life Sciences, Bioinformatics, Microbiology +17

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

Jiarong Guo, Benjamin Bolduc, Ahmed A. Zayed et al. · Microbiome · 2021 · 1.3K citations · Full text

Life Sciences, Bioinformatics, Microbiology +17

Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes

Bing Li, Ying Yang, Liping Ma et al. · The ISME Journal · 2015 · 1.2K citations · Full text

Life Sciences, Genetics, Microbiology +14