An R Wrapper for Bowtie2 and AdapterRemoval


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Documentation for package ‘Rbowtie2’ version 2.8.0

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.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