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

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

Daehwan Kim, Joseph M. Paggi, Chanhee Park, +2

Nature Biotechnology

ChromatinGeneticsGenome StructureGenome AnalysisGenomics +4

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

Daehwan Kim, Geo Pertea, Cole Trapnell, +3

Genome biology

BioinformaticsGene Sequence AnnotationNatural SciencesGeneticsSequence Analysis +12

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Cole Trapnell, Adam Roberts, Loyal A. Goff, +7

Nature Protocols

Differential GeneNatural SciencesGeneticsRna BiologyMolecular Biology +9

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

Mihaela Pertea, Daehwan Kim, Geo Pertea, +2

Nature Protocols

Functional GenomicsNatural SciencesGeneticsRna BiologyMolecular Biology +8

Centrifuge: rapid and sensitive classification of metagenomic sequences

Daehwan Kim, Li Song, Florian P. Breitwieser, +1

Genome Research

EngineeringBurrows-wheeler TransformGeneticsGenomicsBioinformatics Database +16

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

Daehwan Kim, Steven L. Salzberg

Genome biology

Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N

Yun Zhang, Chanhee Park, Christopher Bennett, +2

Genome Research

Centrifuge: rapid and sensitive classification of metagenomic sequences

Daehwan Kim, Li Song, Florian P. Breitwieser, +1

BiologyBioinformatics DatabaseGene Sequence AnnotationMedicineGenetics +13

HISAT-genotype: Next Generation Genomic Analysis Platform on a Personal Computer

Daehwan Kim, Joseph M. Paggi, Steven L. Salzberg

GeneticsGenomicsData StructureGenetic MedicineGenetic Analysis +20