Original implementation by Brian Bushnell (2014): http://seqanswers.com/forums/showthread.php?t=42776
The following tools are compared:
The comparison adds fake truseq adapters, "gruseq", provided by Brian Bushnell, downloaded from: http://seqanswers.com/forums/attachment.php?attachmentid=2993&d=1398383571
A subset of a single sample is from SRA is provided in the repo.
Comment/uncomment the download_FASTQ setting in the config/config.yaml to
download the complete sample from SRA instead. Feel free to replace the URL
with whatever FASTQ file you want.
These plots are produced by the workflow, one for benchmarking results (Snakemake runs each tool three times to assess runtime, CPU and RAM usage), and one plot with adapter removal performance.
Run the benchmarking workflow with something like:
snakemake --use-conda --cores 8