What to choose for the custom WGS bacterial data processing pipeline: KNIME or Galaxy or smth else?
What to choose for the custom WGS bacterial data processing pipeline: KNIME or Galaxy or smth else? Maybe to write a backend bash script to call BBmap, GATK and BedTools and things like that is a better way? What is your expert opinion and experience?
Thx.
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Do you need to do it online? Are you comfortable with the command line? For the latter it's often more convenient to use snakemake, though you can certainly use bash if you prefer.
thx, yes I am able to run command line codes and surely can write some R, Python, PHP, Java, Ruby, JS, SQL and I have forgotten Assemb. and C/C++ since the old days of my studies...what is Snakemake?