# MetaPhlAn 4.2.2 release (initial long-read sequencing support and database update) **URL:** \ **Category:** MetaPhlAn\ **Created:** [June 5, 2025, 7:51pm UTC](https://forum.biobakery.org/t/metaphlan-4-2-2-release-initial-long-read-sequencing-support-and-database-update/8109 "2025-06-05T19:51:54Z")\ **Posts on this page:** 3\ **Page:** 1
**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 5, 2025, 7:51pm UTC](https://forum.biobakery.org/t/metaphlan-4-2-2-release-initial-long-read-sequencing-support-and-database-update/8109/1 "2025-06-05T19:51:54Z")
## Announcement We are pleased to share that MetaPhlAn 4.2.2 is now available, which incorporates taxonomic profiling of long-read metagenomes for the first time and includes a new version of the MetaPhlAn database (vJan25\_202503) containing \>21k new SGBs. For details on MetaPhlan 4, check [announcing MetaPhlAn 4](https://forum.biobakery.org/t/announcing-metaphlan-4/3994) or visit the MetaPhlAn 4 [GitHub repository](https://github.com/biobakery/MetaPhlAn). For the full list of dropped features, modifications, and new features implemented in this new release check the [MetaPhlAn 4.2.2 release notes](https://github.com/biobakery/MetaPhlAn/blob/master/CHANGELOG.md). ## What is new in MetaPhlAn 4.2.2? - Initial support for profiling long-read sequencing metagenomic datasets (with `--long_reads`). This relies on the newly implemented long-read mapper [minimap2](https://github.com/lh3/minimap2). It is also possible to split long reads (with `--split_reads`) in shorter sequences (defined by `--split_readlen`) and map them with [bowtie2](https://github.com/BenLangmead/bowtie2). Check the [full release notes](https://github.com/biobakery/MetaPhlAn/blob/master/CHANGELOG.md) for all long-reads options. - Having now minimap2 as another mapper implemented in MetaPhlAn (in addition to bowtie2), parameters that referred to bowtie2 have now more generic names ( `--bowtie2db` is now `--db_dir` and `--bowtie2out` is now `--mapout`). - The parameter `--unclassified_estimation` is now default. This enables estimation of the portion of unclassified reads, making the relative abundance of detected taxa rescaled accordingly. To restore the previous behavior use `--skip_unclassified_estimation`, which will turn off including an estimate of unclassified reads in the relative abundance profile. ## What has changed in vJan25\_202503 in comparison to vJun23\_202403? ### Expansion and improvement of the genomic database: - ~63k new reference genomes from NCBI - ~416k new MAGs, spanning sea, food, and several animals, among other environments - Improved clustering of SGBs using [skANI](https://github.com/bluenote-1577/skani) ### Expansion and improvement of the markers database: - vJan25 includes 58,331 SGBs, 21,509 more SGBs than in vJun23 - The mapping between the taxonomy of SGBs and the GTDB taxonomy has been updated from GTDB r207 to GTDB r220 - Addition of taxonomy assignment for Viral Sequence Clusters (VSCs) - performed with [geNomad](https://portal.nersc.gov/genomad/pipeline.html) ## How to make use of the MetaPhlAn 4.2.2 updates? - How to install MetaPhlAn 4.2.2 in a new environment: - [MetaPhlAn 4 · biobakery/MetaPhlAn Wiki](https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4.2) - How to update the MetaPhlAn database from the vJun23\_202403 (or earlier) version: - `$ metaphlan --install --force_download` ---
**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 5, 2025, 7:52pm UTC](https://forum.biobakery.org/t/metaphlan-4-2-2-release-initial-long-read-sequencing-support-and-database-update/8109/2 "2025-06-05T19:52:37Z")
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**Author:** ![delahondes](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/delahondes/32/1774_2.png) [@delahondes](https://forum.biobakery.org/u/delahondes)\ **Post date:** [June 11, 2025, 8:16am UTC](https://forum.biobakery.org/t/metaphlan-4-2-2-release-initial-long-read-sequencing-support-and-database-update/8109/3 "2025-06-11T08:16:57Z")
Dear Biobakery Team, Thanks for this release. A small issue for us, and some precisions that might help new comers: it seems the official MetaPhlAn github README is outdated, the correct flag for database install in a custom folder is no more `--bowtie2db` as stated but `--db_dir` When we launched the install doing this: ```sh mkdir /resource/metaphlan422 metaphlan --install --db_dir /resource/metaphlan422 ``` We had this error which has also been reported elsewhere: ```auto Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJan25_CHOCOPhlAnSGB_202503.nwk Wed Jun 11 06:43:56 2025: [Error] EnvironmentError "[Errno 21] Is a directory: '/resource/metaphlan422'" Unable to download http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJan25_CHOCOPhlAnSGB_202503.nwk ``` This is a bug, as obviously the --db\_dir parameter is designed to expect a folder, and all the rest of the install work (and the folder was initially empty when download started, so it’s not a failed download in disguise either). However, the bug is really minor as it can easily being solved by downloading the missing file: ```sh cd /resource/metaphlan422 wget http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJan25_CHOCOPhlAnSGB_202503.nwk ``` After that, all seems fine and metaphlan can be run as stated with: ```sh metaphlan \ --input_type fastq input.fq.gz \ --db_dir /resource/metaphlan422 \ -o profile.txt ```