Doing genome assembly using SPAdes with mate-pair library only on public Galaxy server

Question

[sentausa]

Dear all,

I need to do assembly of Illumina mate-pair reads (from bacterial sample) using SPAdes, and I'm thinking to use public Galaxy server so that I won't need to install SPAdes myself. However, when I used the only public Galaxy server where I can find SPAdes, it gave an error:

== Error == you should specify at least one paired-end or unpaired library (only mate-pairs libraries were found)!

After searching in SPAdes website, I concluded that the error came since the SPAdes version that I used in the public server was 3.0.0, while the manual states that "SPAdes should not be used if only mate-pairs [...] are available."

A manual of a later SPAdes version (3.1.0) indicates that now it "supports mate-pair only assembly". So, I wonder if anyone is aware of a public Galaxy server which has SPAdes 3.1.0. Or else, is it possible to do something with my mate-pair data so that it can run with SPAdes 3.0.0?

Thank you very much for your help.

[martenson]

What about running your own Galaxy (local or cloud) and installing SPAdes (in various versions) from the Galaxy ToolShed?

Also there is a dedicated Galaxy Biostar where you could check how difficult it would be to update spades to newest version in the Galaxy Tool Shed.

[sentausa]

Thanks. I think it's a good alternative.

Answer 1

[anton]

Please note that in order to use SPAdes 3.1+ for mate-pair only assemblies you need to have the so-called "high quality mate pairs". Right now such mate pairs can only be generated using Nextera mate pair protocol. Everything else would give you suboptimal assemblies.