We'll use base R only in this recipe, so you don't need to install any packages. You will need the reference genome FASTA file in datasets/ch8/ecoli_genome.fa and the datasets/ch8/ERR019653.fastq,gz file that we created in the Finding experiments and reads from SRA/ENA recipe. This recipe also requires a working copy of BWA and samtools on your system. The web pages for these pieces of software are at http://samtools.sourceforge.net/ and http://bio-bwa.sourceforge.net/. If you have conda installed, you can install it with conda install -c bioconda bwa and conda install -c bioconda samtools.