Question: Where to get some example metagenomics data?
0
gravatar for mschmid
4.9 years ago by
mschmid150
Switzerland
mschmid150 wrote:

To test an algorithm I need some random metagenomics data. It should be whole genome and not just 16S or other marker gene. Is there any resource where I can find such data?

Ideally the data is already assembled to contigs. It does not matter if the assembly is not very good, but at least a basic assembly would be nice. Raw data does not work for my test.

database metagenomics • 2.4k views
ADD COMMENTlink modified 4.9 years ago by Manu Prestat4.0k • written 4.9 years ago by mschmid150
0
gravatar for glihm
4.9 years ago by
glihm620
France
glihm620 wrote:

Hi, 

Here you have lot's of metagenomics data, from various ecosystems: https://www.ebi.ac.uk/metagenomics/

Is that what you need? If you clic on a sample, you have various things available. So, perhaps some files contain assembled contigs, for example: a sample files list.

ADD COMMENTlink written 4.9 years ago by glihm620
0
gravatar for Manu Prestat
4.9 years ago by
Manu Prestat4.0k
Lyon, France
Manu Prestat4.0k wrote:

You can download more than 28K metagenomes on MG-RAST. If this is of interest, I made a REST based program which allows the query and downloads of MG-RAST metagenomes.

https://github.com/alunem/bioman/blob/master/mgrast/bmn-mgrast.py

 

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by Manu Prestat4.0k
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