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.
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.
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.