Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).
Stranger Things: unexpected limitations of popular tools
The comparison between HISAT2 and Tophat2
Run mutltiple Fastq files on Hisat2
What is the difference between HISAT2 index "genome.tran" and "genome"
Too low mapping percentage using HISAT2 on human reference genome.
hisat2-build indexing produces more than 8 output files
Hisat2 versus Bowtie2
Which strand specific option need to be used with HISAT2?
Compatibility between my reference genome and GTF file
HISAT2 rna-strandness option
How to resync paired-end data?
Is there a way to separate highly similar strains from metatranscriptomic data using HISAT2?
Could not locate a HISAT2 index to basename
HISAT2 : Differences in paired and unpaired rates
Strand-option in hisat2
fastq.gz Error: Not in gzip format
HISAT2 and Stringtie: difference in Stringtie results when using pre-built indexes or creating new ones in HISAT2
Mapping RNA-Seq data on genome from another species
Hisat R strandness aligning same strand as F strandness, how to do it correctly?
HISAT2 error running both --dta and --min and --max-intronlen