Design, construction, and in vivo augmentation of a complex gut microbiome

The Sequence Alignment/Map format and SAMtools

Heng Li, Alec Wysoker, Tim Fennell et al. · Bioinformatics · 2009 · 67.5K citations · Full text

Life Sciences, Bioinformatics, Genetics +17

Fast gapped-read alignment with Bowtie 2

Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 61.1K citations

Life Sciences, Bioinformatics, Molecular Biology +11

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Anton Bankevich, Sergey Nurk, Dmitry Antipov et al. · Journal of Computational Biology · 2012 · 27.2K citations

Life Sciences, Bioinformatics, Microbiology +17

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

A human gut microbial gene catalogue established by metagenomic sequencing

Junjie Qin, Ruiqiang Li, Jeroen Raes et al. · Nature · 2010 · 11.7K citations · Full text

Life Sciences, Genetics, Microbiology +17