This pipeline enables you to benchmark kASA together with other tools e.g.: Kraken, Kraken2, Clark, ganon, Centrifuge, MetaCache.
These pipelines assume that you are working in a Linux environment since most of the other tools do too.
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Download and install the tools you wish to benchmark. If some tool is not of interest to you, write "" instead of the path inside the config file.
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Install Snakemake (we recommend that you install conda first and then use
pip3 install snakemake --userinside this conda environment. Please note, that you have to activate the conda environment every time you want to use snakemake.). -
Check the config file(s) which contain parameters that need to be changed for your platform (like paths, RAM, number of threads, etc.)
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Call one of the snakefiles with
snakemake -s <snakefile>.
You might want to use .clean.sh to remove all benchmark related files.
This will evaluate time and memory consumption as well as create profiles in cami format for all results of every tool.
It downloads genomes given in the CAMI2 Gastrointestinal tract toy data set, creates indices for every tool from them and checks against all fastq files of this toy set.
Finally, OPAL can be called to compare profiling capability of all tested tools and settings. For every tool and setting (e.g. with threshold or without), a *_all.cami file will be created. Therefore please call the script as follows (OPAL needs to be in the PATH variable): scripts/callOPAL.sh opal.py genomes/pacbio/taxonomic_profile_all.txt all results/ results/OPAL_all.
The results are given inside the folder results (which is created during the benchmark). Scripts for the evaluation can be found inside the scripts folder. Measurements of time and memory consumption are saved inside the benchmarks folder for the index creation and identification step of every tool.
If the evaluation of the Centrifuge script should fail then the building step of the tool had a hiccup and "forgot" to assign certain tax IDs. Just run the building step again and it should work...
For kASA, setting the flag 128 to 1 in the config runs an additional extended version with a maximum k of 25.
NOTE: taxid 272556 for CP008984.1 had to be inserted manually