Question: Doing genome assembly using SPAdes with mate-pair library only on public Galaxy server
1
gravatar for sentausa
3.9 years ago by
sentausa630
France
sentausa630 wrote:

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 mate-pair galaxy assembly • 3.9k views
ADD COMMENTlink modified 3.7 years ago by anton40 • written 3.9 years ago by sentausa630
1

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

Also there is dedicated Galaxy Biostar at https://biostar.usegalaxy.org/ where you could check how difficult it would be to update spades to newest version in the Galaxy Tool Shed.

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by martenson380

Thanks. I think it's a good alternative.

ADD REPLYlink written 3.8 years ago by sentausa630
2
gravatar for anton
3.7 years ago by
anton40
United States
anton40 wrote:

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.

ADD COMMENTlink written 3.7 years ago by anton40
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