Rhisat2

Rhisat2 provides an R interface to the HISAT2 spliced short-read aligner, containing wrapper functions to create a genome index and to perform read alignment to the generated index.

Key Features:

• Genome Index Creation: The package provides wrapper functions to create a genome index for use with the HISAT2 aligner.
• Read Alignment: The package provides wrapper functions to perform spliced short-read alignment to a generated genome index.

Scientific Applications:

• Spliced Read Alignment: Enables alignment of spliced short-read sequencing data to a reference genome within the R environment.

Methodology:

The package wraps the HISAT2 spliced short-read aligner by Kim et al. (2015) through R functions that interface with the underlying HISAT2 algorithms for genome indexing and alignment.