Assembly analysis
MGnify assembly analysis consists of three pipelines: the assembly annotation pipeline, VIRify, and the mobilome annotation pipeline (MAP). Their results are presented together on MGnify, but each pipeline has its own purpose and version.
Assembly analysis accepts assembled metagenomic and metatranscriptomic datasets.
Analyses
- Assembly annotation pipeline provides quality-control, taxonomic, functional, pathway, and systems annotations for the assembled contigs.
- VIRify detects, annotates, and classifies viral sequences in the metagenomic assembly.
- Mobilome Annotation Pipeline (MAP) identifies mobile genetic elements and generates virulence-associated annotation at protein level. MAP incorporates results from VIRify.
These pipelines run as connected analyses, and their results are accessible from the corresponding MGnify website and FTP server.
Submitting data to be assembled
Users can request assembly of their own raw sequencing reads or publicly available datasets using the “Request analysis” section of the MGnify home page. User-owned raw reads, with host sequences removed, must be uploaded to ENA before an assembly request can be submitted. Alternatively, pre-assembled datasets, including those produced using other assembly algorithms, can be analysed.
Each pipeline is versioned independently. See Comparability between pipeline versions for an explanation of MGnify pipeline versions.
Citation
@online{2026,
author = {, MGnify},
title = {Assembly Analysis},
date = {2026-10-15},
url = {https://docs.mgnify.org/src/docs/analysis/version6/assembly.html},
langid = {en}
}