How to calculate organism relative abundance from Illumina metagenomic data?

[nkuyfq]

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.

[rnaeye]

take a look at metaphlan. you may need more to normalize things but it might be a good starting point.

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

Also,

http://qiime.org/

[nkuyfq]

Thanks for your reply.

Metaphlan is quite excellent and I will try it out.

Question 1: In addition to Bacteria and Archaea, has Metaphlan already covered virus and fungi? (As I have no access to its original Nature Methods paper, I have to ask the question here?)

Question 2: Can Metaphlan handle pair-end sequences?

[nkuyfq]

take a look at metaphlan. you may need more to normalize things but it might be a good starting point.

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

Also,
http://qiime.org/

Thanks for your reply.

Metaphlan is quite excellent and I will try it out.

Question 1: In addition to Bacteria and Archaea, has Metaphlan already covered virus and fungi? (As I have no access to its original Nature Methods paper, I have to ask the question here?)

Question 2: Can Metaphlan handle pair-end sequences?

[patouch74]

Hi, I don't understand how is calculated the abundance in Metaphlan.
Someone can explain to me please ?

[rnaeye]

I think they have Nature Methods paper published on it. I believe they are mapping to unique regions of each species. It may not give very accurate information on absolute and relative levels. I am no expert in the field though.