# Would MetaPhlAn support PE mapping in future version?
**URL:** https://forum.biobakery.org/t/would-metaphlan-support-pe-mapping-in-future-version/4422
**Category:** MetaPhlAn
**Created:** [November 21, 2022, 3:10am UTC](https://forum.biobakery.org/t/would-metaphlan-support-pe-mapping-in-future-version/4422 "2022-11-21T03:10:57Z")
**Posts on this page:** 9
**Page:** 1
### Author:  [@cquxiaoy](https://forum.biobakery.org/u/cquxiaoy)
#### Post date: [November 21, 2022, 3:10am UTC](https://forum.biobakery.org/t/would-metaphlan-support-pe-mapping-in-future-version/4422/1 "2022-11-21T03:10:57Z")
As I know, current MetaPhlAns do not support pairwise sequence alignment. Would it be possible in future version ?
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### Author:  [@Dario](https://forum.biobakery.org/u/Dario)
#### Post date: [November 26, 2022, 9:00pm UTC](https://forum.biobakery.org/t/would-metaphlan-support-pe-mapping-in-future-version/4422/2 "2022-11-26T21:00:47Z")
I hope so. It would waste less disk space if it was not necessary to make concatenated files.
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### Author:  [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)
#### Post date: [November 28, 2022, 10:57am UTC](https://forum.biobakery.org/t/would-metaphlan-support-pe-mapping-in-future-version/4422/3 "2022-11-28T10:57:34Z")
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:
```auto
$ 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:
```auto
$ cat metagenome_*.fastq | metaphlan --bowtie2out metagenome.bowtie2.bz2 --nproc 5 --input_type fastq -o profiled_metagenome.txt
```
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### Author:  [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)
#### Post date: [November 28, 2022, 10:59am UTC](https://forum.biobakery.org/t/would-metaphlan-support-pe-mapping-in-future-version/4422/4 "2022-11-28T10:59:26Z")
Hi @cquxiaoy
Currently, this option is not possible but we will consider its implementation in the future version
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### Author:  [@cquxiaoy](https://forum.biobakery.org/u/cquxiaoy)
#### Post date: [November 29, 2022, 1:08am UTC](https://forum.biobakery.org/t/would-metaphlan-support-pe-mapping-in-future-version/4422/5 "2022-11-29T01:08:21Z")
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?
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### Author:  [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)
#### Post date: [November 30, 2022, 8:26am UTC](https://forum.biobakery.org/t/would-metaphlan-support-pe-mapping-in-future-version/4422/6 "2022-11-30T08:26:30Z")
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
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### Author:  [@cquxiaoy](https://forum.biobakery.org/u/cquxiaoy)
#### Post date: [November 30, 2022, 8:30am UTC](https://forum.biobakery.org/t/would-metaphlan-support-pe-mapping-in-future-version/4422/7 "2022-11-30T08:30:50Z")
Do you mean they should still be counted as 1.0 after setting bowtie2 a right argument ?
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### Author:  [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)
#### Post date: [November 30, 2022, 8:32am UTC](https://forum.biobakery.org/t/would-metaphlan-support-pe-mapping-in-future-version/4422/8 "2022-11-30T08:32:21Z")
Exactly, I would not count them differently if executed bowtie2 with the paired-end specification
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### Author:  [@cquxiaoy](https://forum.biobakery.org/u/cquxiaoy)
#### Post date: [November 30, 2022, 8:39am UTC](https://forum.biobakery.org/t/would-metaphlan-support-pe-mapping-in-future-version/4422/9 "2022-11-30T08:39:20Z")
Allright, thank you very much !