| .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 |