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The Rhisat2 R package provides an R interface to the hisat2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.

Source code

The source code for hisat2 v2.1.0 was obtained from on October 17, 2018.

Based on the discussion at, the following small modification was made to allow compilation:

In the file src/aligner_result.cpp, line 1267

flag > 0

was replaced by

flag[0] != '\0'

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Rhisat2 documentation built on Nov. 8, 2020, 5:49 p.m.