Benchmark for PLASS paper
The following tools have to be installed in order to create and execute the prochlorococcus benchmark/
mmseqs2
prodigal
bbmap
After installing the tools execute the following commands to setup the benchmarking data:
:::bash
git clone https://github.com/martin-steinegger/plass-analysis
cd plass-analysis/Prochloroccus
chmod u+x *
makeProchlorococcus.sh
Each tool can be executed separately by calling the respective shell scripts e.g. runPlassProchloroccus.sh, runMetaspadesProchloroccus.sh, ... However the assembler binary has to be in the $PATH variable.