Food Control · 2017 · 26 citations · 34 references
AgricultureFood ScienceMicrobiologyFood HygieneFood MicrobiologyFood SafetyFoodborne Disease SurveillanceFoodborne Pathogen DetectionFoodborne PathogensMicrobial ContaminationMicrobial Food SafetyMicrobiological Food SafetyBacterial Contamination Of FoodsFood Hygiene MonitoringFoodborne Bacterial Disease EpidemiologyFoodborne Illness EpidemiologyFoodborne Source TrackingListeria DetectionListeria Monocytogenes Contamination
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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
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li, Richard Durbin · Bioinformatics · 2009 · 62.8K citations · Full text
Prokka: rapid prokaryotic genome annotation
Torsten Seemann · Bioinformatics · 2014 · 19.6K citations
Fast and accurate long-read alignment with Burrows–Wheeler transform
Heng Li, Richard Durbin · Bioinformatics · 2010 · 12.9K citations · Full text
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Daniel R. Zerbino, Ewan Birney · Genome Research · 2008 · 9.7K citations · Full text