bowtie2_index

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. bowtie2-build is used to build the index files.
Recipe source code: https://github.com/rworkflow/ReUseDataRecipe/blob/master/bowtie2_index.R (opens new window)
Data source: https://bowtie-bio.sourceforge.net/bowtie2/index.shtml (opens new window)

plot

Inputs

	label	type	description
genome	reference genome	File	The reference genome file

Outputs

	label	type	description
btIdx	bowtie2 index	File[]	A list of bowtie index files

Example:

bowtie2_index <- recipeLoad('bowtie2_index')
bowtie2_index$genome <- 'GRCh38.primary_assembly.genome.fa' ## need to be a valid file path
getData(bowtie2_index, outdir = 'data/folder', notes = c('bowtie2_index', 'GRCh38.primary_assembly'))

## Get data from local catch
dataUpdate('data/folder')
dataSearch(c('bowtie2_index', 'GRCh38'))