Question: calculating abundance of metagenomes
0
gravatar for biobiu
11 months ago by
biobiu120
United States
biobiu120 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 • 595 views
ADD COMMENTlink modified 9 days ago by colindaven2.3k • written 11 months ago by biobiu120
1

Have you seen MetaPhlAn v.2.0?

ADD REPLYlink written 11 months ago by genomax85k

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

ADD REPLYlink written 11 months ago by biobiu120
1

Why not to use marker genes methods?

ADD REPLYlink written 11 months ago by Costadia10

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

ADD REPLYlink written 11 months ago by biobiu120
0
gravatar for Nari
11 days ago by
Nari880
United States
Nari880 wrote:

https://github.com/HRGV/phyloFlashphyloFlash which uses SSU 16S against SILVA db.

ADD COMMENTlink written 11 days ago by Nari880
0
gravatar for colindaven
9 days ago by
colindaven2.3k
Hannover Medical School
colindaven2.3k wrote:

It's not really intended to answer your question, and you've probably solved this by now, but our pipeline can do the alignment and your intended normalization (including number of reads and genome length):

https://github.com/MHH-RCUG/Wochenende

Seeing as you have a custom output, you'll need to create a reference sequence (combine contigs to "genomes" by removing headers) and index it.

ADD COMMENTlink written 9 days ago by colindaven2.3k
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