Links

KimLab - https://kim-lab.org
- lab github - https://github.com/DaehwanKimLab
- github for HISAT2 - https://github.com/DaehwanKimLab/hisat2
hisat-genotype - https://daehwankimlab.github.io/hisat-genotype
- github for hisat-genotype - https://github.com/DaehwanKimLab/hisat-genotype
Lyda Hill Department of Bioinformatics at UT Southwestern Medical Center - https://www.utsouthwestern.edu/departments/bioinformatics
Center for Computational Biology at Johns Hopkins University - http://www.ccb.jhu.edu

Funding

This work was supported in part by the National Human Genome Research Institute under grants R01-HG006102 and R01-HG006677, and NIH grants R01-LM06845 and R01-GM083873 and NSF grant CCF-0347992 to Steven L. Salzberg and by the Cancer Prevention Research Institute of Texas under grant RR170068 and NIH grant R01-GM135341 to Daehwan Kim

Getting Help

Please use hisat2.genomics@gmail.com for private communications only. Please do not email technical questions to HISAT2 contributors directly.

Publications

Zhang, Y., Park, C., Bennett, C., Thornton, M. and Kim, D. Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N. Genome Research 31, 1290-1295 (2021).
Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915 (2019).
Kim D, Langmead B and Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 2015
Pertea M, Kim D, Pertea G, Leek JT and Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature Protocols 2016