The completed macronuclear genome of a model ciliate Tetrahymena thermophila and its application in genome scrambling and copy number analyses

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

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Daehwan Kim, Geo Pertea, Cole Trapnell et al. · Genome biology · 2013 · 13.7K citations · Full text

Life Sciences, Bioinformatics, Genetics +14

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research

Bioinformatics · 2005 · 12.1K citations · Full text

Life Sciences, Bioinformatics, Biology +12

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

Bruce J. Walker, Thomas Abeel, Terrance Shea et al. · PLoS ONE · 2014 · 10.2K citations · Full text

Life Sciences, Bioinformatics, Microbiology +17

Canu: scalable and accurate long-read assembly via adaptive <i>k</i> -mer weighting and repeat separation

Sergey Koren, Brian P. Walenz, Konstantin Berlin et al. · Genome Research · 2017 · 8.2K citations · Full text

Life Sciences, Bioinformatics, Biology +16