HOW-TO

First, clone or download the repository to a location on your system.

Second, define environmental variables within your system architecture.

1. Export the path to the benchmarking base directory:

export BENCHPATH=/path/to/benchmarking

2. Export the number of threads to use for testing:

export THREADS=8

3. Export the path to these tools in your working environment:

export BOWTIE2_DIR=/usr/local/bowtie2/2.3.4.2/binary
export SAMTOOLS_DIR=/usr/local/samtools/1.9/binary/bin

4. Export the path to these aligners in your working environment:

export RAZERS3_DIR=/usr/local/razers3/3.5.8/binary/bin
export BISMARK_DIR=/usr/local/bismark/0.20.0/binary
export BSSEEKR_DIR=/usr/local/bsseeker/2.1.5/binary
export BWAMETH_DIR=/usr/local/bwameth/0.2.2/binary
export ERNEBS5_DIR=/usr/local/erne/2.1.1/binary/bin
export GEM3MAP_DIR=/usr/local/gem/3.6/binary/bin
export GSNAP_DIR=/usr/local/gsnap/2018-07-04/binary/bin
export LASTMAP_DIR=/usr/local/last/950/binary/bin
export SEGEMAP_DIR=/usr/local/segemehl/0.3.2/binary
export BSMAP_DIR=/usr/local/bsmap/2.6/binary

Third, now follow each step sequentially for the species of interest:

For each species

1. Navigate to reads directory, follow commands.sh to generate reads
2. Navigate to genome directory, follow commands.sh to build genome indexes
3. Navigate to mapping directory, follow commands.sh to carry out read alignments
4. Navigate to analysis directory, follow commands.sh to generate tables/graphics