# hisat2_index

HISAT2 is a fast and sensitive 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. hisat2-build is used to build the index files.
Recipe source code: https://github.com/rworkflow/ReUseDataRecipe/blob/master/hisat2_index.R (opens new window)
Data source: http://daehwankimlab.github.io/hisat2/ (opens new window)

# plot

## hisat2_index

# Inputs

label type description
genome reference genome File The reference genome file

# Outputs

label type description
htIdx hisat2 index File[] A list of index files

# Example:

recipeLoad('hisat2_index.R', return = TRUE)
hisat2_index$genome <- 'GRCh38.primary_assembly.genome.fa'
getData(hisat2_index, outdir = 'data/folder', notes = c('hisat2_index', 'GRCh38.primary_assembly'))