Rarefaction curve of Shotgun metagenome

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5.0 years ago

jeccy.J ▴ 60

We have done a large scale shotgun metagenome over 100 samples and analysed using metaphlan2. Can anybody help me out how to perform a Rarefaction analysis of metaphal2 output, as i can did not see anything motioned about Rarefaction on metaphaln web page. In case of amplicon we can subsample the reads and perform the analysis but what should we do in shotgun metagenome sequencing?

sequence metagenome • 2.1k views

ADD COMMENT • link updated 4.8 years ago by Biostar 20 • written 5.0 years ago by jeccy.J ▴ 60

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Export the output to biom and import into MEGAN. MEGAN can do rarefaction analysis, alpha and beta diversities. Qiime2/Qiime can also import biom files and do the analysis.

ADD REPLY • link 4.8 years ago by cpad0112 21k

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Hi cpad0112!!! Can I do the rarefaction analysis of shotgun sequences with MEGAN?

ADD REPLY • link 4.4 years ago by dpc ▴ 250

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we did it with 16s with megan. But due to licensing issues, we shifted to qiime2 pipeline. If you are new, you can follow this protocol (galaxy and mothur): https://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html

ADD REPLY • link 4.4 years ago by cpad0112 21k

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Hi cpad0112!!! Can I do the rarefaction analysis of shotgun sequences with MEGAN? I have shotgun metagenome sequence analysed by MetaPhlAn.

Thanks, DC7

ADD REPLY • link 4.4 years ago by dpc ▴ 250

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