Complete read-to-reference alignment with external programs using the following steps:

1. Set up the files and executable paths:

bwa <- "/Users/macleand/miniconda2/bin/bwa"
samtools <- "/Users/macleand/miniconda2/bin/samtools"
reference <- file.path(getwd(), "datasets", "ch8", "ecoli_genome.fa")

2. Prepare the index command and run:

command <- paste(bwa, "index", reference)
system(command, wait = TRUE)

3. Prepare the alignment command and run:

reads <- file.path(getwd(), "datasets", "ch8", "ERR019653.fastq.gz")
output <- file.path(getwd(), "datasets", "ch8", "aln.bam")
command <- paste(bwa, "mem", reference, reads, "|", samtools, "view -S -b >", output)
system(command, wait = TRUE)