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.
I could not log in to
MScBioinf@quince-srv2.eng.gla.ac.ukWhat is the password.