Where to get some example metagenomics data?

Question

[mschmid]

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.

Answer 1

[glihm]

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 click on a sample, you have various things available. So, perhaps some files contain assembled contigs, for example: a sample files list.

Answer 2

[Manu Prestat]

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