Skip to content
R wrapper around the hisat2 aligner.
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
R
inst/extdata
man
src
tests
vignettes
.BBSoptions
.Rbuildignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS
README.md
appveyor.yml

README.md

Rhisat2

Build Status AppVeyor build status Code coverage

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 https://ccb.jhu.edu/software/hisat2/index.shtml on October 17, 2018.

Based on the discussion at https://github.com/BenLangmead/bowtie2/issues/81, 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'
You can’t perform that action at this time.