Question: How to calculate organism relative abundance from Illumina metagenomic data?
0
gravatar for nkuyfq
5.5 years ago by
nkuyfq60
China
nkuyfq60 wrote:

I have got pair-end metagenomic data (2 x 100bp) generated by Illumina Hiseq 2000 of several samples. Human sequences have been removed and I aligned the rest reads to bacteria reference genomes. I want to calculate organism content (namely, relative abundance) of each sample so that I can use this information in further comparative metagenomics analysis.

The question is how to calculate organism relative abundance from the rest reads. Note that different samples may have different sequencing levels, normalization may be needed. I need organism relative abundance that could correct for different sequencing levels in these samples. Is there a software which can handle this?

p.s.:Qin's paper entitled 'A human gut microbial gene catalogue established by metagenomic sequencing' talks about how relative abundance was calculted, however, there is no much detail provided. It's quite confusing.

As I am building my own analysis pipline, online resources might not fit for me.

ADD COMMENTlink modified 4.7 years ago by Len Trigg1.3k • written 5.5 years ago by nkuyfq60
1

You can try MEGAN or MG-RAST.

ADD REPLYlink written 5.5 years ago by JC8.8k

Thanks for your reply.

1)MEGAN seems to give absolute read counts to me, and I don't know whether it has corrected for different sequencing levels in my samples.

2)As I am building my own analysis pipline, online resources might not fit for me

 

ADD REPLYlink written 5.5 years ago by nkuyfq60

I see, maybe you can use QIIME or Kraken.
 

ADD REPLYlink written 5.4 years ago by JC8.8k

Thanks, I will have a try.

ADD REPLYlink written 5.4 years ago by nkuyfq60

Hi,

I am also doing same kind of analysis.  What do you mean by "different samples may have different sequencing levels" ?

Thanks,

D

 

 

ADD REPLYlink written 4.7 years ago by deepthithomaskannan270
2
gravatar for Brett Kennedy
5.5 years ago by
Salt Lake City, UT
Brett Kennedy50 wrote:

Check out Kraken:

http://genomebiology.com/2014/15/3/R46

https://github.com/DerrickWood/kraken

Recently published out of the Salzberg lab.  It's easy to run and install, if a bit resource intensive.  I would be skeptical of anything mapping below species, but to the genus level it's reasonably accurate.  Not to mention blazing fast.

Edit:

Kraken won't deliver immediate relative abundance, but an identification for each reference, which will likely recaputulate the relative abundance taken together.  

MetaPhilAn is another tool that is specifically for relative abundance and is worth a look.

http://huttenhower.sph.harvard.edu/metaphlan

ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by Brett Kennedy50

+1 for metaphlan

ADD REPLYlink written 5.5 years ago by Andreas2.4k
1
gravatar for Len Trigg
4.7 years ago by
Len Trigg1.3k
New Zealand
Len Trigg1.3k wrote:

You can also try the metagenomics functions from Real Time Genomics. The RTG species tool takes SAM/BAM mapped to a reference species database and calculates abundances either by abundance of dna or by organism (taking genome lengths into account). If your reference includes taxonomic information (RTG provides pre-built ones that include bacteria and viruses) this is also taken into account, and reporting is both via tsv and krona visualization. (RTG Core is available free for non-commercial academic use).

 

ADD COMMENTlink written 4.7 years ago by Len Trigg1.3k
0
gravatar for nkuyfq
5.5 years ago by
nkuyfq60
China
nkuyfq60 wrote:

Both Kraken and Metaphlan seem good. I will try them out.

ADD COMMENTlink written 5.5 years ago by nkuyfq60

Metaphlan seems only cover Bacteria and Archaea, which is a limiting factor for its use in Viral and Fungal metagenome.

Kraken is likely to be a resource-intensive software, but it's quite fast.

ADD REPLYlink written 5.5 years ago by nkuyfq60
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