Doing genome assembly using SPAdes with mate-pair library only on public Galaxy server
Entering edit mode
8.0 years ago
sentausa ▴ 640

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.

SPAdes Galaxy mate-pair Assembly • 5.6k views
Entering edit mode

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.

Entering edit mode

Thanks. I think it's a good alternative.

Entering edit mode
7.8 years ago
anton ▴ 60

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.


Login before adding your answer.

Traffic: 1868 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6