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H. sapiens, UCSC hg19 7.0 GB
M. musculus, UCSC mm10 6.4 GB

The current version of HISAT does not use some of the files in the index, so the actual memory requirement is much lower than the index size. For example, the memory footprint of HISAT for the human genome is about 4.3GB.

Related Tools

  • Bowtie2: Ultrafast read alignment
  • TopHat2: Spliced read mapper for RNA-Seq
  • Cufflinks: Isoform assembly and quantitation for RNA-Seq
  • StringTie: Transcript assembly and quantification for RNA-Seq




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