Phylum And Genus Abundance Calculation In 16S Rna And/Or Wgs

Question

[Dhruv Sakalley]

This question is rather specific Genus and phylum abundance was estimated after normalizing for genome size for the former, and for 16S gene copy number for the latter. [http://www.nature.com/nature/journal/v473/n7346/full/nature09944.html#/abundant-functions-from-low-abundance-microbes]

Can someone please detail on the steps needed for such a calculation given the raw reads and contigs? Which tools would form the pipeline? What would be the thresholds used for coverage and identity?

Here are the resources: http://www.bork.embl.de/Docu/Arumugam_et_al_2011/

PS: SMASHCommunity is suggested but, nothing has been detailed for calculation of genus/ phylum abundance. Also dependencies of SMASH communities include deadlinks/moved weblinks making it unusable.

Answer 1

[umer.zeeshan.ijaz]

Hi Dhruv,

I regularly use CREST and RDP Classifier for generating abundance profiles for 16S RNA (at Phylum, Class, Order, Family and Genus level). You can use MetaPhlAn, TAXAassign (my own software), and MEGAN for WGS. To help people understand how to process metagenomic datasets, I have put up two tutorials (using an example dataset) on my website and discuss how you can go from Raw Reads to Abundance Tables + afterwards, how you can then perform multivariate statistical analysis using the abundance table generated from these classifiers against environmental parameters that you recorded. The links are given below, if you follow the same structure as I have you can simply copy/paste the commands from my tutorials.

• 16S rRNA Amplicons Processing Workflow for Illumina: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/Illumina_workflow.html

• WGS Short-read based Workflow (MetaPhlAn pipelines): http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/Metagenomics_tutorial.html

• WGS Contig-based Workflow (CONCOCT): https://github.com/BinPro/CONCOCT

• Generating abundance tables from RDP and CREST: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/oneliners.html?#PHYLOMAP

Best Wishes, Umer

[Naren]

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