Would MetaPhlAn support PE mapping in future version?

As I know, current MetaPhlAns do not support pairwise sequence alignment. Would it be possible in future version ?

I hope so. It would waste less disk space if it was not necessary to make concatenated files.

Hi @Dario
Concatenation of paired end files is not necessary to execute metaphlan.
In those cases, you could use two options:

  1. Pass the name of the input read files separated by comma to the script. E.g:
$ metaphlan metagenome_1.fastq,metagenome_2.fastq --bowtie2out metagenome.bowtie2.bz2 --nproc 5 --input_type fastq -o profiled_metagenome.txt
  1. Pass the content of the input read files by the standard input. E.g:
$ cat metagenome_*.fastq | metaphlan --bowtie2out metagenome.bowtie2.bz2 --nproc 5 --input_type fastq -o profiled_metagenome.txt

Hi @cquxiaoy
Currently, this option is not possible but we will consider its implementation in the future version

Is it an alternative method to count the matched paired end reads as 0.5 (for each) while the single end reads as 1.0 in the marker2nreads count?

Not really, the best alternative would be to execute bowtie2 with the same presets and database but specifying the paired-end reads as -1 and -2 and the execute metaphlan over the generated sam file

Do you mean they should still be counted as 1.0 after setting bowtie2 a right argument ?

Exactly, I would not count them differently if executed bowtie2 with the paired-end specification

Allright, thank you very much !