MetaPhlAn

Topic	Replies	Views	Activity
MetaPhlAn 4.2.2 release (initial long-read sequencing support and database update) 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_…	1	2330	June 11, 2025
Announcing MetaPhlAn 4 MetaPhlAn 4 Release Notes The new MetaPhlAn 4 integrates information from both metagenome assemblies and microbial isolate genomes for improved and more comprehensive metagenomic taxonomic profiling (https://doi.org/10.1…	6	4952	June 8, 2023
Announcing MetaPhlAn 3.1 MetaPhlAn 3.1 / HUMAnN 3.1 Release Notes MetaPhlAn 3.1 and HUMAnN 3.1 represent a moderate update to the bioBakery 3 software and databases. This update is based on improvements in our ability to align NCBI-sourced micro…	1	1057	August 4, 2022
Update for sgb to GTDB Translation File - r220	6	276	June 16, 2026
Downloading MetaPhlAn 4 database	6	1572	June 11, 2026
Error in downloading metaphlan database	0	19	June 11, 2026
Metaphlan 4.2.4: TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType	2	22	May 27, 2026
Getting split reads from MetaPhlAn 4.2.4?	0	22	May 26, 2026
Downloading metaphlan4 SGB genomes	9	495	May 25, 2026
Difference in sequencing depth	3	76	May 25, 2026
Total Bacteria species relative abundance no longer sums to 1 after converting the SGB profile to GTDB	18	1480	May 24, 2026
Strain taxonomic level Identification	4	155	May 22, 2026
SGB Newick file labels	3	86	May 22, 2026
MetaPhlAn4 (mpa_vJun23_CHOCOPhlAnSGB_202307): unexpected behavior with fix_relab_mpa4.py	6	60	May 22, 2026
Beta diversity in metaphlan 4.2.4 doesn't work becuase of rbiom upgrade?	1	22	May 22, 2026
Correupt bowtie2 index file? metaphlan error	1	29	May 22, 2026
Nanopore long-reads analysis with Metaphlan4.2.2	0	25	May 12, 2026
mpa_vJan25_CHOCOPhlAnSGB_202503.fna not downloaded in the .tar file	2	81	May 11, 2026
Matching/linking profiled species using MetaPhlAn3 (v3.0.1) to MetaPhlAn (4.2.4),database: mpa_vJan25_CHOCOPhlAnSGB_202503	0	30	April 9, 2026
Metaphlan 3.0.7 related problem with deep sequenced wgs file	0	18	April 3, 2026
Inquiry regarding qPCR primer design for uncharacterized SGBs using the CHOCOPhlAn marker database	0	17	April 1, 2026
HUMANN3.9 cannot recognize MetaPhlAn 4.2.2 output file	11	560	April 1, 2026
Metaphlan genus level relative abundance not summing up to 100% and possible database problem	10	944	March 23, 2026
calculate_diversity.R script is not working properly	1	67	March 15, 2026
MetaPhlAn removes the database then complains there is no database	0	73	March 12, 2026
Newick tree for mpa_vJan25_CHOCOPhlAnSGB_202503	1	48	March 6, 2026
biobakery_workflows 3.1 with MetaPhlAn 3 vs 4 — what are the differences?	0	28	February 24, 2026
Reverse forward reads as input in MetaPhlAn 4	2	58	February 17, 2026
Extending the metaphlan4 database (Jan2025) to include subspecies	2	82	February 13, 2026
Metaphlan flags and parameters for extreme metagenomes	1	28	January 30, 2026

MetaPhlAn 4.2.2 release (initial long-read sequencing support and database update)

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_…

1

2330

June 11, 2025

Announcing MetaPhlAn 4

MetaPhlAn 4 Release Notes The new MetaPhlAn 4 integrates information from both metagenome assemblies and microbial isolate genomes for improved and more comprehensive metagenomic taxonomic profiling (https://doi.org/10.1…

6

4952

June 8, 2023

Announcing MetaPhlAn 3.1

MetaPhlAn 3.1 / HUMAnN 3.1 Release Notes MetaPhlAn 3.1 and HUMAnN 3.1 represent a moderate update to the bioBakery 3 software and databases. This update is based on improvements in our ability to align NCBI-sourced micro…