Combined virome analysis and metagenomic sequencing to reveal the viral communities and risk of virus–associated antibiotic resistance genes during 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

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen, Heiko A. Schmidt, Arndt von Haeseler et al. · Molecular Biology and Evolution · 2014 · 27.5K citations · Full text

Life Sciences, Bioinformatics, Biology +15

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

Donovan H. Parks, Michael Imelfort, Connor T. Skennerton et al. · Genome Research · 2015 · 12.8K citations · Full text

Life Sciences, Biology, Microbiology +17

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct <i>de Bruijn</i> graph

Dinghua Li, Chi-Man Liu, Ruibang Luo et al. · Bioinformatics · 2015 · 10K citations · Full text

Life Sciences, Bioinformatics, Genome Assembly +11

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

Dongwan Kang, Feng Li, Edward Kirton et al. · PeerJ · 2019 · 3.9K citations · Full text

Life Sciences, Bioinformatics, Microbiology +15