Doing network analysis and metagenomic reconstruction using qiime2?

[arjun_nbaim (Arjun Singh)]

Hello,
Greetings from ICAR-NBAIM to whole q2 team

Our group has recently conducted a training programme at ICAR-NBAIM, Mau, India on the usage of qiime2 pipeline for microbial community analysis. But we missed out on network analysis part and metagenome reconstruction part, as we have no idea on how to implement q2 outputs for this kind of analysis. If you have any links pertaining to this please help us in getting through.

With kind regards,
Arjun Singh

[ebolyen (Evan Bolyen)]

Hi @arjun_nbaim and the ICAR-NBAIM team!

@arjun_nbaim

Our group has recently conducted a training programme at ICAR-NBAIM, Mau, India on the usage of qiime2 pipeline for microbial community analysis.

Awesome!

@arjun_nbaim

But we missed out on network analysis part and metagenome reconstruction part, as we have no idea on how to implement q2 outputs for this kind of analysis. If you have any links pertaining to this please help us in getting through.

Unfortunately, we don't have any finished network analysis plugins (at this time!). A good tool to try might be SpiecEasi (R library). You'll need to export your feature table into something R can consume (the qiime2R package can make your life easier there).

As for metagenome reconstruction, we have essentially nothing for that at this time, I'm also not familiar enough with the field to recommend anything in particular.

If anyone else has suggestions, please jump in!