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Where to get some example metagenomics data?

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.

metagenomics database
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updated by Ram Ram • written by mschmid mschmid

2 answers

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.

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updated by Ram Ram • written by glihm glihm

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

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updated by Ram Ram • written by Manu Prestat Manu Prestat

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