Are you trying to use the Public Galaxy or a local install? There
are several assemblers with Galaxy Wrappers on the Galaxy
ToolShed (e.g. Roche "Newbler", and MIRA 3) which you could
add to your own local Galaxy if you have one.

There are wrappers for ABySS as well. These assemblers are generally for genome data.

For transcriptome data, galaxy-central provides a wrapper for the Trinity assembler.

However, do novo genome assembly can be very computationally
demanding, so not many Galaxy Instances will want to offer it.

If you don't want to/can't set up a local instance for assembly, consider using a cloud instance:


Good luck,