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

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:

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

## Get data from local catch
dataUpdate('data/folder')
dataSearch(c('hisat2_index', 'GRCh38.primary_assembly'))