Question: calculating abundance of metagenomes
0
gravatar for biobiu
23 days ago by
biobiu100
United States
biobiu100 wrote:

Hi, We performed shotgun metagenomics for dozens of stool samples. Next, we assembled the reads into contigs and binned the contigs to reconstruct the genomes. We want to use the reconstructed metagenomes in order to calculate the abundance of the microbes they represent in all samples.

  1. Is there any recommended aligner (and parameters) for such task? (considering that we align against not-full genomes, multimapping etc.)
  2. I came across some studies that calculated relative abundance by dividing the number of reads aligned to a metagenome by the total number of reads of a sample. Any Idea why genome length was not also taken into account?
  3. Is there any reason to calculate absolute abundance in such case? (maybe for downstream analyses/tools?)

Thanks!

alignment assembly • 150 views
ADD COMMENTlink modified 20 days ago by Costadia10 • written 23 days ago by biobiu100
1

Have you seen MetaPhlAn v.2.0?

ADD REPLYlink written 23 days ago by genomax70k

Thanks. Yes I've seen, we think on a way to estimate abundance without using marker genes.

ADD REPLYlink written 22 days ago by biobiu100
1

Why not to use marker genes methods?

ADD REPLYlink written 20 days ago by Costadia10

We assume that we have un-characterized species of bacteria and non-bacterial genomes.

ADD REPLYlink written 20 days ago by biobiu100
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