# Combine metaphlan and humann

**URL:** <https://forum.biobakery.org/t/combine-metaphlan-and-humann/8136>\
**Category:** HUMAnN\
**Created:** [June 12, 2025, 8:04pm UTC](https://forum.biobakery.org/t/combine-metaphlan-and-humann/8136 "2025-06-12T20:04:29Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![mattpich](https://avatars.discourse-cdn.com/v4/letter/m/77aa72/32.png) [@mattpich](https://forum.biobakery.org/u/mattpich)\
**Post date:** [June 12, 2025, 8:04pm UTC](https://forum.biobakery.org/t/combine-metaphlan-and-humann/8136/1 "2025-06-12T20:04:29Z")

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Hi,

I’m new to BioBakery and would really appreciate some guidance.

I’m currently working with paired-end reads and looking to integrate **MetaPhlAn** and **HUMAnN** in my workflow. To optimize time and computational resources, I was wondering:  
**Is it possible to use the SAM output from MetaPhlAn as input for HUMAnN, while still preserving the accuracy and integrity of the results?**

Thank you in advance for your help and insights!

===  
version

- Metaphlan 3.6.1
- Humann 4.1.1

example of code:

```auto
metaphlan \
	--input_type fastq \
	--read_min_len 50 \
	--bowtie2db ${metaphlan_reffolder} \
	--index ${metaphlan_refname} \
	--bowtie2out bowtie2.log \
	--samout samout.bz2 \
	-t rel_ab_w_read_stats \
	--nproc ${threads} \
	-o tmp_metaphlan_profile.tsv \
	${R1},${R2}

### - decompress alignment file 
bunzip2 samout.bz2

### - run humann using metaphlan alignment file
	humann \
	-i samout \
	--threads ${threads} \
	--taxonomic-profile tmp_metaphlan_profile.tsv \
	--memory-use maximum \
	--nucleotide-database ${humann_nucleotidedb} \
	--protein-database ${humann_proteindb} \
	--output-format tsv \
	--output-basename test \
	--output tmp.out

```

---

<div class="post-metadata">

**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\
**Post date:** [June 13, 2025, 7:37pm UTC](https://forum.biobakery.org/t/combine-metaphlan-and-humann/8136/2 "2025-06-13T19:37:24Z")

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If you’re running MetaPhlAn outside of HUMAnN you can pass the resulting taxonomic profile to HUMAnN via the `--taxonomic-profile` flag. While HUMAnN _can_ read SAM results, you would not want to start from the MetaPhlAn SAM, as those would only contain alignments of reads to marker genes.

---

<div class="post-metadata">

**Author:** ![mattpich](https://avatars.discourse-cdn.com/v4/letter/m/77aa72/32.png) [@mattpich](https://forum.biobakery.org/u/mattpich)\
**Post date:** [June 15, 2025, 7:30pm UTC](https://forum.biobakery.org/t/combine-metaphlan-and-humann/8136/3 "2025-06-15T19:30:27Z")

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> [@franzosa](#):
>
> `--taxonomic-profile`

Sounds good. Thanks for the clear answer and the explanation!