Question: What to choose for the custom WGS bacterial data processing pipeline: KNIME or Galaxy or smth else?
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gravatar for hrenchert747
2.9 years ago by
hrenchert74750
hrenchert74750 wrote:

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.

wgs pipeline galaxy next-gen knime • 695 views
ADD COMMENTlink written 2.9 years ago by hrenchert74750
1

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.

ADD REPLYlink written 2.9 years ago by Devon Ryan89k

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?

ADD REPLYlink written 2.8 years ago by hrenchert74750
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