Bioconductor package: an R wrapper for Bowtie2 and AdapterRemoval

The Rbowtie2 package provides an R interface to the bowtie2 short read aligner by Langmead et al. (2009), and the AdapterRemoval package by Schubert, Lindgreen, and Orlando (2016). The Rbowtie2 package allows users to remove adapter sequences from reads, build bowtie2 indexes (.bt2 or .bt2l), and to create bowtie2 alignment files (.sam or .bam).

The package interfaces with the bowtie2 and bowtie2-build wrapper scripts provided in the bowtie2 v2.4.4 source code. The bowtie2 wrapper script is a Perl script and the bowtie2-build wrapper script is a Python script. Most versions of MacOS and Linux distributions come with a version of Perl and Python pre-installed. On Windows, both Perl and Python do not come pre-installed and they must be downloaded and installed manually. If either Perl or Python are not installed on your system follow the links below to download and install them.

Python: https://www.python.org/downloads/

Perl: https://www.perl.org/get.html

The package also uses samtools to create bam files if it is present on the system. The reason for this is explained under the Bam File Creation heading. However, samtools is completely optional and the package can be used without it. To download samtools follow the link below.

samtools: http://www.htslib.org/download/

The Rbowtie2 package attempts to use samtools to create the bam file if present on the system. This method of creating the bam file avoids the need to create an intermediate sam file which might be infeasable depending on the size of the file and the available memory on the system. If samtoolsis not found on the system, the package attempts to create the bam file via Rsamtools which requires that an intermediate sam file be created prior to the bam file being created.

The Rbowtie2 package uses the bowtie2 v2.4.4 source code which was obtained from https://sourceforge.net/projects/bowtie-bio/. The folders doc, example, scripts, and some non-code files were deleted to reduce the package size.