Fiji: an open-source platform for biological-image analysis

Johannes Schindelin, Ignacio Arganda‐Carreras, Erwin Frise, +13

Nature Methods

BiologyBiological-image AnalysisImage AnalysisEngineeringMicroscope Image Processing +6

NIH Image to ImageJ: 25 years of image analysis

Caroline A Schneider, Wayne Rasband, Kevin W. Eliceiri

Nature Methods

Image AnalysisMachine VisionData ScienceEngineeringPattern Recognition +6

Fast gapped-read alignment with Bowtie 2

Ben Langmead, Steven L. Salzberg

Nature Methods

Long-read SequencingSequence AssemblyNatural SciencesComputational BiologyMolecular Biology +5

SciPy 1.0: fundamental algorithms for scientific computing in Python

Nature Methods

DADA2: High-resolution sample inference from Illumina amplicon data

Benjamin J. Callahan, Paul J. McMurdie, Michael Rosen, +3

Nature Methods

Illumina Amplicon DataOmics DatasetsSpectral SearchingOmicsBiostatistics +3

HISAT: a fast spliced aligner with low memory requirements

Daehwan Kim, Ben Langmead, Steven L. Salzberg

Nature Methods

Hardware SecurityEngineeringHardware AccelerationHigh-performance ArchitectureComputer Engineering +5

ModelFinder: fast model selection for accurate phylogenetic estimates

Subha Kalyaanamoorthy, Bùi Quang Minh, Thomas K. F. Wong, +2

Nature Methods

BiologyPhylogeneticsNatural SciencesEvolutionary BiologyComputational Biology +4

UPARSE: highly accurate OTU sequences from microbial amplicon reads

R. C. Edgar

Nature Methods

Long-read SequencingAccurate Otu SequencesSequence AnalysisMicrobiologyGenomics +3

Fast and sensitive protein alignment using DIAMOND

Benjamin Buchfink, Chao Xie, Daniel H. Huson

Nature Methods

Structural BioinformaticsProtein FoldingSensitive Protein AlignmentNatural SciencesMolecular Biology +5

Mapping and quantifying mammalian transcriptomes by RNA-Seq

A Mortazavi, Brian A. Williams, Kenneth McCue, +2

Nature Methods

Functional GenomicsGeneticsTranscriptomics TechnologyMammalian TranscriptomesLong Non-coding Rna +5