# Recommended versions of required programs
- Python 2.6.1
- Bowtie 0.11.3
- Samtools 0.1.6

# Default alignment program
Bowtie short-read aligner

# Configuration
- Update the paths in the alignment script, i.e. align.bow
- Build the indexes for the reference genome (h_sapiens_asm) and the breakpoint junction library (bplib)

# Execution
./bpmap <output:dirname/basename> <query_read_file:fastq/fasta>...
