This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Rarefaction curve of Shotgun metagenome

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
• 2,818 views • link
updated by Biostar Biostar • written by jeccy.J jeccy.J

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.

• 0 views • link
written by cpad0112 cpad0112

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

• 0 views • link
written by dpc dpc

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

Thanks, DC7

• 0 views • link
written by dpc dpc

0 answers

No answers yet.

Log in to answer this question.

More posts like this