What to choose for the custom WGS bacterial data processing pipeline: KNIME or Galaxy or smth else?

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8.5 years ago

hrenchert747 ▴ 50

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.

next-gen pipeline knime galaxy wgs • 1.6k views

ADD COMMENT • link 8.5 years ago by hrenchert747 ▴ 50

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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.

ADD REPLY • link 8.5 years ago by Devon Ryan 104k

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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 REPLY • link 8.4 years ago by hrenchert747 ▴ 50

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