I want to map WGS against a reference but the species is not on the drop down reference list and it says I should contact Galaxy Team. Please advise

Assuming you want to use bowtie2. Above the dropdown reference list there is another option. By default it is set to “Use a built-in genome index”. You can change this to “Use a genome from the history and build index”. Now you can upload your own reference.

Details here FAQ: How to use Custom Reference Genomes? Or see custom-genome for more examples. If you sort by recent topics, you find some with demonstrations.

Galaxy Community Help

Mapping against a WGS reference

usegalaxy.eu support

custom-genome, mapping

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