# An R Wrapper for Bowtie2 and AdapterRemoval

## Documentation for package ‘Rbowtie2’ version 2.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.callbinary | Make system call for binaries
adapterremoval_usage | Print available arguments for adapterremoval
adapterremoval_version | Print version information of adapterremoval
bowtie2 | Interface to bowtie2 of bowtie2-2.2.3
bowtie2-build | Interface to bowtie2-2.4.4 build function
bowtie2_build | Interface to bowtie2-2.4.4 build function
bowtie2_build_usage | Print available arguments that can be passed to bowtie2_build()
bowtie2_samtools | Interface to bowtie2-2.4.4 align function
bowtie2_usage | Print available arguments that can be passed to bowtie2()
bowtie2_version | Print version information of bowtie2-2.4.4
checkFileCreatable | Check if file is creatable
checkFileCreateable | Check if file is creatable
checkFileExist | Check if file exists
checkIndexType | Determine bowtie2 index type
checkPathExist | Check if path exists
checkSamtoolsExists | Check if samtools exists on the system
identify_adapters | identify adapters for paired-end reads
remove_adapters | Interface to bowtie2 of adapterremoval-2.2.1a