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Increasing automation in Bioinformatics

What do veterans of the community think of the advent of automation and streamlined bioinformatics tools such as Galaxy or automated pipelines such as the new Braker4?

galaxy braker automation
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updated by shelkmike shelkmike • written by thrivenow • thrivenow

3 answers

Automation is very important and pipelines lead to higher quality analyses with less tedious re-running of tools with different parameters.

This has all been exhaustively documented in the scientific literature in the last 10+ years.

Reproducibility has improved dramatically over what was available from 2005-2015.

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written by colindaven colindaven

most " veterans of the community" won't use galaxy or any GUI , they will use a workflow manager like snakemake or nextflow.

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written by Pierre Lindenbaum Pierre Lindenbaum

Ready-made pipelines are OK if you're doing something routine. In my experience, it's often better to make your own pipeline that accounts for the specifics of your task and samples.

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written by shelkmike shelkmike

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