where to download the reference_genome for strainer?

[Ming Liao]

Hello,

I am currently trying to use strainer_src in Metaphlan2.

In the toy example provided in the tutorial, the reference genome directory contains two files: G0000273725.fna.bz2,
s__Bacteroides_caccae_G0000273735.fna.bz2

Can anyone explain these files a little bit? Is the G0000273725 just another name for s__Bacteroides_caccae, or one of many such numbers ?

Most importantly, where can I download this kind of reference genome data? By the way, the specie I am interested with most is E.coli.

Thanks,

Ming

[Duy Tin Truong]

Hi Ming,

Two files are the same but I added the prefix to remember that it is a reference genome from s__Bacteroides_caccae.

You can download the reference genomes from ncbi, for example:

http://www.ncbi.nlm.nih.gov/assembly/?term=Escherichia%20coli

Cheers,

Tin

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