Question: What platform similar to Galaxy can handle multiple batch processing of bacterial genomes, mutation profiling and GWAS?
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gravatar for bioinform
20 months ago by
bioinform20
bioinform20 wrote:

What platform similar to Galaxy can handle multiple batch processing of bacterial genomes, mutation profiling and GWAS? It seems that Galaxy can`t take the input of 1000 SRA ids and output annotated mutation profiling lists. Need a better tool for a batch processing of the NGS data.

ADD COMMENTlink modified 20 months ago by colindaven1.1k • written 20 months ago by bioinform20

multiple batch processing of bacterial genomes

This is quite aspecific, would be best if you specify what kind of processing you are aiming for. Anyway, since you want to process many samples in parallel it looks like you need a server.

ADD REPLYlink written 20 months ago by WouterDeCoster37k
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gravatar for colindaven
20 months ago by
colindaven1.1k
Hannover Medical School
colindaven1.1k wrote:

This is not easy, but is possible in Galaxy with collections. There was a talk at the galaxy conference about it.

See the abstract and linked slides in the following.

https://gcc2017.sched.com/event/BH73/galaxy-at-scale-analyzing-thousands-of-single-cell-transcriptomes

You will probably end up writing something like this yourself, but 1000 bacteria is not too many. I have worked with 100s in the past myself without too many issues.

ADD COMMENTlink written 20 months ago by colindaven1.1k
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