Nature Medicine · 2021 · 233 citations · 61 references
Life SciencesImmunologyMicrobiologyMedical MicrobiologyMicrobiome ResearchMucosal ImmunologyAirway DiseasesObstructive Lung DiseaseRespiratory DiseaseRespiratory InfectionsRespiratory MicrobiomeRespiratory PathologyChronic Obstructive Pulmonary Disease MicrobiomeFunctional MicrobiomicsLung MicrobiomePulmonary ExacerbationsRespiratory Microbiology
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Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony Bolger, Marc Lohse, Björn Usadel · Bioinformatics · 2014 · 69.7K citations · Full text
The Sequence Alignment/Map format and SAMtools
Heng Li, Alec Wysoker, Tim Fennell et al. · Bioinformatics · 2009 · 67.5K citations · Full text
Fast gapped-read alignment with Bowtie 2
Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 61.1K citations
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Paul Shannon, Andrew Markiel, Owen Ozier et al. · Genome Research · 2003 · 54.3K citations · Full text
KEGG: Kyoto Encyclopedia of Genes and Genomes
Minoru Kanehisa · Nucleic Acids Research · 2000 · 39.2K citations · Full text