An R Wrapper for Bowtie2 and AdapterRemoval

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Documentation for package ‘Rbowtie2’ version 2.12.0

• 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