| bwa_aln | R wrapper to run BWA alignment tool BWA-backtrack |
| bwa_build_index | R wrapper to create BWA index files |
| bwa_mem | R wrapper to run BWA alignment tool BWA-MEM |
| bwa_sam | R wrapper to convert bwa aln output to SAM format |
| xa2multi | Unpack multiple alignments stored in BWA output |