Entering edit mode
7.7 years ago
What NGS tools management system has the largest built-in choice of aligners and variant callers? I need to choose between Galaxy, KNIME, Taverna, GenePattern, Kepler, Chipster. Tavaxy and Yabi. Need to process WGS tuberculosis ,sra and ,fastq to align against reference genomes and report mutation lists.
Is that really the important question? Wouldn't you rather just know which one(s) provide the toolset you need?
to me it is important, have seen people who had invested a half of life in what brings nothing, but errors, you can delete, I will not consider that an offence, thx
Your approach should be to pick the set of tools that work best with your data. GATK for example works best with human DNA data, and low coverage alignment is done best by samtools.
You should not go with what gives you what you think is the best result unless you're sure your mechanism for judging the goodness of that method is solid. Something that gives you more variants may not be the best tool, for example. Instead, you should find out which tool goes best with the experiment and use that.
First, figure out which tools you need and how they work. Trying to set up these system without being familiar with the tools that you need is going to be extremely difficult (much harder than using the tools themselves).