Analysis pipeline v6
Overview
The latest MGnify analysis service (version 6) offers pipelines for three different data types: amplicon, raw metagenomic/metatranscriptomic reads, and assemblies.
Analysed assembled datasets are complemented by VIRify for viral sequence detection and the Mobilome annotation pipeline, both accessible in the same web view.
“MGnify analysis service v6” is the name of this collection of analysis pipelines. Each pipeline and associated service has its own version number.
Analysis pipelines documentation
MGnify provides three analyses, selected according to the type of sequence data being analysed.
- Amplicon analysis pipeline: analyses amplicon sequencing reads and provides taxonomic profiles, including ASV analysis for supported 16S and 18S datasets.
- Raw reads analysis pipeline: analyses short or long metagenomic and metatranscriptomic reads to provide taxonomic and functional profiles.
- Assembly analysis: analyses assembled metagenomic and metatranscriptomic contigs with the assembly annotation pipeline, VIRify, and the Mobilome Annotation Pipeline, providing taxonomic, functional, pathway, systems, viral, and mobile genetic element annotations.
See Submitting data to be assembled for how to request an assembly.
Current MGnify Analysis versions
Pipeline repositories
Each of the pipelines that constitute the service is versioned independently. Their repositories provide software releases and pipeline documentation; the latest software release may differ from the version deployed on MGnify.
- Amplicon analysis pipeline
- Raw reads analysis pipeline
- Assembly annotation pipeline (assembly-analysis-pipeline)
- VIRify
- Mobilome Annotation Pipeline
Comparability between pipeline versions
When comparing results, use the first two numbers of the pipeline version. For example, analyses produced by releases v6.1.4 and v6.1.5 both belong to analysis version v6.1 and can be compared.
- The first two numbers identify the analysis version, such as
v6.1. - The final number identifies the exact software release. Patch releases within the same analysis version produce comparable results.
- Results from different analysis versions, such as
v6.0andv6.1, should not be assumed to be directly comparable due to potential differences in pipeline outputs.
For example, MGnify describes the amplicon pipeline as analysis version v6.2, and records the full three-part software version for reproducibility.
Pipeline-specific changelogs provide details about software releases: amplicon analysis, assembly annotation, VIRify, and mobilome annotation. Raw reads release information is available in its repository.
Changes through pipeline versions
Amplicon Analysis Pipeline
Version 6.2 [September 2026]
Version 6.2 improved annotation support for ITS, LSU, and 5.8S-containing sequences. The ITS workflow now recognises and masks 5.8S regions, enabling the analysis of 5.8S+ITS datasets, while a bug preventing LSU annotation has been fixed. Reference databases now use a target field so that SSU and LSU databases are applied only to matching sequence types, reducing unnecessary searches; ITS databases continue to run across sequence types because ITS amplicons may contain adjacent ribosomal regions.
Version 6.1 [April 2026]
Version 6.1 improved completeness, reporting, and configurability. All ASVs are now published, including those without taxonomic assignments, so no detected sequence diversity is excluded. DADA2 reporting now includes selected truncation points and read counts from intermediate filtering stages, improving transparency and troubleshooting. MAPseq database selection and DADA2 execution are also more configurable, allowing the pipeline to support a wider range of datasets and analysis requirements.
Citation
@online{2026,
author = {, MGnify},
title = {Analysis Pipeline V6},
date = {2026-10-15},
url = {https://docs.mgnify.org/src/docs/analysis/version6/analysis.html},
langid = {en}
}