Using paired reads in Metaphlan 2

[Theo Allnutt]

Hi,

I have read the manual, but I'm not clear on how to use paired reads. I have my reads in an interleaved fasta file:

>read1 1:etc
AGTAGATAGTA.....
>read1 2:etc
ACTTGCTCTCT.....

but I could use any format. My current command line is:

metaphlan2.py 1.fasta -o 1.txt --input_type multifasta --nproc 24

This seems to give a reasonable basic output, but I can't tell if it is using the paired information in the file.

Thanks.

[Duy Tin Truong]

Hi Theo,

MetaPhlAn2 considers all reads as single reads. You can run them as:

metaphlan2.py 1.fasta,2.fasta -o all.txt --input_type multifasta --nproc 24

metaphlan2.py 1.fastq,2.fastq -o all.txt --input_type multifastq --nproc 24

Cheers,

Tin

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[Theo Allnutt]

Hi,

I see. Perhaps you should remove or change the sentence in your documentation: "MetaPhlAn 2 can also natively handle paired-end metagenomes, and, more generally, metagenomes stored in multiple files (but you need to specify the --bowtie2out parameter):" because it makes it sound like metaphlan2 can actually use paired read information.

Thanks,

Theo

[Duy Tin Truong]

Hi Theo,

Thank you for your suggestion but it may mean that metaphlan2 can accept as input the paired-end metagenomes or multiple metagenomes stored in multiple files.

Cheers,

Tin

[tatsuya unno]

So metaphlan knows which reads are PE? (assuming checking sequence IDs)
Since PE reads are from one single DNA fragment, they should be assigned with the same taxonomy.

Thanks,
Tatsu

[Nicola Segata]

Hi Tatsuya, MetaPhlAn accepts paired end reads but we do not explicitly make us of them: we do not check whether the two ends map against the same marker. Because of the definition of markers in MetaPhlAn two ends should not map against different markers, but it can instead happen that one of the two ends does not map because it falls outside the sequence of the marker.

Best

Nicola 

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Nicola Segata, PhD
Assistant Professor and Principal Investigator

Laboratory of Computational Metagenomics
Centre for Integrative Biology
University of Trento, Italy

Email: nicola...@unitn.it

Web: http://segatalab.cibio.unitn.it

Skype: nicola.segata

Phone: +39 0461 285218