Assembly annotation pipeline

Description of the MGnify v6.0 assembly annotation pipeline.

Author

Affiliation

Published

October 15, 2026

The MGnify v6.0 assembly annotation pipeline (GitHub repository: assembly-analysis-pipeline) analyses assembled metagenomic and metatranscriptomic datasets, providing functional, taxonomic, pathway, and systems annotation for assembled contigs. It is one of the three pipelines of the assembly analysis. The other two, VIRify and the Mobilome annotation pipeline, are run as separate pipelines on assemblies and are presented in the same web view.

Here, v6.0 identifies the analysis version. See the pipeline repositories for software releases and pipeline documentation.

MGnify uses miassembler to assemble sequencing reads. See Submitting data to be assembled for how to request an assembly.

Results available on MGnify

For each analysed assembly, MGnify displays and provides downloads for:

Assembly quality-control summaries and the filtered contig sequences.
Predicted coding sequences and extracted ribosomal and other non-coding RNA sequences.
Contig-level taxonomic assignments and interactive Krona visualisations.
Functional annotations for predicted proteins, including InterPro, eggNOG, Gene Ontology, KEGG Orthology, Rhea reactions, and run_dbCAN annotations.
Pathway and systems annotations, including biosynthetic gene clusters, Genome Properties, KEGG modules, and DRAM summaries.
An integrated GFF3 annotation summary combining most of the annotations generated by the pipeline.

Features

The MGnify assembly analysis pipeline v6.0 provides the following key features:

Assembly quality control, including optional decontamination of human, PhiX, and custom contaminant sequences
CDS prediction with the MGnify Combined Gene Caller
Taxonomic assignment of assembled contigs with Contig Annotation Tool (CAT)
Functional annotation with InterProScan, eggNOG Mapper, GO Slims, run_dbCAN, KEGG Orthologs, and RHEA
Biosynthetic gene-cluster annotation with antiSMASH and SanntiS
KEGG module completeness analysis from KEGG Ortholog annotations
Consolidation of generated annotations into a single GFF file

Technical details and results reference

Schema

Tools

Tool	Version	Purpose
antiSMASH	8.0.1	Tool for the identification and annotation of secondary metabolite biosynthesis gene clusters
boto3	1.35.37	AWS SDK for Python used to access EBI FIRE S3 storage for assembly file downloads
CAT_pack	6.0	Taxonomic classification of the contigs in the assembly
cmsearchtbloutdeoverlap	0.09	Deoverlapping of cmsearch results
csvtk	0.31.0	A cross-platform, efficient, and practical CSV/TSV toolkit
Combined Gene Caller - Merge	1.4.17	Combined gene caller merge script used to combine predictions of Pyrodigal and FragGeneScanRS (this tool is part of the mgnify-pipelines-toolkit)
Diamond	2.1.11	Used to match predicted CDS against the CAT reference database for the taxonomic classification of the contigs
DRAM	1.3.5	Summarizes annotations from multiple tools like KEGG, Pfam, and CAZy
easel	0.49	Extracts FASTA sequences by name from a cmsearch deoverlap result
extractcoords	1.2.11	Processes output from easel-sfetch to extract SSU and LSU sequences (this tool is part of the mgnify-pipelines-toolkit).
FragGeneScanRs	1.1.0	CDS calling; this tool specializes in calling fragmented CDS
generategaf	1.2.0	Script that generates a GO Annotation File (GAF) from an InterProScan result TSV file (this tool is part of the mgnify-pipelines-toolkit).
Genome Properties	2.0	Uses protein signatures as evidence to determine the presence of each step within a property
Infernal - cmscan	1.1.5	RNA sequence searching
InterProScan	5.76-107.0	Functionally characterizes nucleotide or protein sequences by scanning them against the InterPro database.
HMMER	3.4	Used to annotate CDS with KO
Krona	2.8.1	Krona chart visualisation
kegg-pathways-completeness	1.3.0	Computes the completeness of each KEGG pathway module based on KEGG orthologue (KO) annotations.
MGnify pipelines toolkit	1.2.0 to 1.4.24	Collection of tools and scripts used in MGnify pipelines. Each step uses a fixed release; the default release is 1.2.0.
minimap2	2.29-r1283	A versatile pairwise aligner for genomic and spliced nucleotide sequences. Used in the assembly decontamination subworkflow
MultiQC	1.29	Tool to aggregate bioinformatic analysis results.
Owltools	2024-06-12T00:00:00Z	Tool utilized to map GO terms to GO-slims
Pyrodigal	3.6.3	CDS calling
pigz	2.3.4	A parallel implementation of gzip for modern multi-processor, multi-core systems
QUAST	5.2.0	Tool used evaluates genome assemblies, it’s part of the pipeline QC module.
run_dbCAN	5.1.2	Annotation tool for the Carbohydrate-Active enZYmes Database (CAZy)
SeqKit	2.8.0	Used to manipulate FASTA files
SanntiS	0.9.4.1	Tool used to identify biosynthetic gene clusters
tabix	1.21	Generic indexer for TAB-delimited genome position files
Genome Tools - gff3validator	1.6.5	Used to validate the analysis summary GFF file
jq	1.5	Used to concatenate the chunked antiSMASH json results

Reference databases

This pipeline uses several reference databases, you can find the list of them in the follow table. The databases marked with ^* are downloaded and post-processed by the Microbiome Informatics reference-databases-preprocessing-pipeline. Our team also stores ready to use version of these databases in EBI’s FTP server.

Reference Database	Version	Purpose	Download
Rfam covariance models	15	rRNA covariance models	ftp://ftp.ebi.ac.uk/pub/databases/Rfam/15.0/Rfam.cm.gz
Rfam clan info	15	rRNA clan information	ftp://ftp.ebi.ac.uk/pub/databases/Rfam/15.0/Rfam.clanin
InterProScan	5.76-107.0	InterProScan reference database	ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.76-107.0/
eggNOG-mapper	5.0.2	eggNOG-mapper annotation databases and Diamond	https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.12#requirements
antiSMASH	8.0.1	The antiSMASH reference database	https://docs.antismash.secondarymetabolites.org/install/#antismash-standalone-lite
KOFAM^*	2025-04	KOfam - HMM profiles for KEGG/KO. Our reference generation pipeline generates the required files	https://github.com/EBI-Metagenomics/reference-databases-preprocessing-pipeline
GO Slims^*	20160705	Metagenomics GO Slims	ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipelines/tool-dbs/goslim/20160705/goslim_20160705.tar.gz
run_dbCAN	4.1.4-V13	Pre-built run_dbCAN reference database	ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipelines/tool-dbs/dbcan/dbcan_4.1.4_V13.tar.gz
CAT_Pack	2025_01	CAT/BAT/RAT NCBI taxonomy pre-made reference database	https://github.com/MGXlab/CAT_pack?tab=readme-ov-file#downloading-preconstructed-database-files
DRAM	1.3.0	DRAM databases	https://github.com/WrightonLabCSU/DRAM/wiki#dram-setup

Output files

qc

The qc directory contains output files related to the quality control steps of the pipeline, from the contig length filtering by seqkit, to the quality assessment done by QUAST. The qc directory contains these files and directories:

├── qc
│   ├── ERZ12345_filtered_contigs.fasta.gz
│   ├── ERZ12345_filtered_contigs.fasta.gz.gzi
│   ├── ERZ12345_filtered_contigs.fasta.gz.fai
│   ├── ERZ12345_quast_stats.tsv.gz
│   ├── multiqc_report.html
│   ├── multiqc_data/
│   └── decontamination/
├── cds
├── taxonomy
├── rnas
├── functional-annotation
├── pathways-and-systems
└── annotation-summary

Output files

ERZ12345_filtered_contigs.fasta.gz: This FASTA file contains the final processed contigs. Contigs shorter than 500 bases and those with a proportion of ambiguous bases higher than 10% are removed first. If decontamination is enabled, contigs aligning to the PhiX, human, or host reference genomes are also removed. It is bgzip-compressed to allow random access via the accompanying index files.
ERZ12345_filtered_contigs.fasta.gz.gzi: This file is a compression index for the bgzip-compressed filtered contigs FASTA file.
ERZ12345_filtered_contigs.fasta.gz.fai: This file is a FASTA index for the bgzip-compressed filtered contigs FASTA file.
ERZ12345_quast_stats.tsv.gz: This compressed tsv file contains the QUAST summary output, giving an assessment of the quality of the contigs of this assembly.
multiqc_report.html: This html file contains the MultiQC report for that assembly. It combines outputs from multiple tools, including QUAST (run both before and after quality control during assembly preprocessing), decontamination summary tables (if contaminated contigs were detected), and records of the software versions used by the pipeline.
multiqc_data/: This directory contains the input files used by MultiQC to generate its report.
decontamination/: This directory contains TSV files with details of contigs that were removed during decontamination steps (only created if contaminated contigs are found).

Decontamination output files

When the decontamination step is enabled and contaminated contigs are detected, TSV files are created in the decontamination/ subdirectory. Each TSV file contains three columns: sequence_id (contig identifier), query_coverage (coverage of the alignment), and identity (percentage identity of the alignment). Contigs are classified as contaminated if they have query coverage ≥ 0.3 (30%) and identity ≥ 0.4 (40%) when aligned to the respective reference genome. These are the default values of the min_qcov and min_pid parameters.

The following files may be created:

ERZ12345_aligned_to_human.tsv.gz: Contigs identified as contaminated with human DNA.
ERZ12345_aligned_to_phix.tsv.gz: Contigs identified as contaminated with PhiX DNA.
ERZ12345_aligned_to_contaminant.tsv.gz: Contigs identified as contaminated with custom host/contaminant DNA.

These files are integrated into the MultiQC report as interactive tables under the “Decontamination Summary” section.

cds

The cds directory contains output files related to the combined gene caller subworkflow, which calls genes using both Pyrodigal and FragGeneScanRs, which are a Python interface to Prodigal and a Rust re-implementation of FragGeneScan, respectively. The identified genes are then merged, and the resulting outputs are saved in this directory in three different formats.

├── qc
├── cds
│   ├── ERZ12345_predicted_orf.ffn.gz
│   ├── ERZ12345_predicted_cds.faa.gz
│   └── ERZ12345_predicted_cds.gff.gz
├── taxonomy
├── rnas
├── functional-annotation
├── pathways-and-systems
└── annotation-summary

Output files

ERZ12345_predicted_orf.ffn.gz: This FASTA file contains the nucleotide sequences of each predicted Open Reading Frame (ORF) by the combined gene caller, making up the collection of genes detected in the assembly.
ERZ12345_predicted_cds.faa.gz: This FASTA file contains the amino acid sequences of each predicted ORF, making up the collection of proteins detected in the assembly.
ERZ12345_predicted_cds.gff.gz: This gff file contains the Coding DNA Sequences regions in the GFF3 format.

taxonomy

The taxonomy directory contains the contig taxonomy assignments from CAT_pack, as well as visualisations generated with Krona.

├── qc
├── cds
├── taxonomy
│   ├── ERZ12345_contigs_taxonomy.tsv.gz
│   ├── ERZ12345.krona.txt.gz
│   └── ERZ12345.html
├── rnas
├── functional-annotation
├── pathways-and-systems
└── annotation-summary

Output files

ERZ12345_contigs_taxonomy.tsv.gz: This tsv file contains the output from CAT_pack that describes taxonomy assignments to contigs in the assembly.
ERZ12345.krona.txt.gz: This compressed txt file contains the Krona text input that is used to generate the Krona HTML file. It contains the distribution of the different taxonomic assignments from the CAT_pack output.
ERZ12345.html: This html file contains the Krona HTML file that interactively displays the distribution of the different taxonomic assignments from CAT_pack.

rnas

The rnas directory contains FASTA files produced by EXTRACTCOORDS, including SSU, LSU, bacterial, archaeal, eukaryotic, 5S, 5.8S, and other ncRNA sequences. Each file is optional and is only created when the corresponding RNA category is detected.

├── qc
├── cds
├── taxonomy
├── rnas
│   ├── ERZ12345_SSU.fasta.gz
│   ├── ERZ12345_LSU.fasta.gz
│   ├── ERZ12345_*rRNA_bacteria*.fasta.gz
│   ├── ERZ12345_*rRNA_archaea*.fasta.gz
│   ├── ERZ12345_*rRNA_eukarya*.fasta.gz
│   ├── ERZ12345_*5S.fasta.gz
│   ├── ERZ12345_*5_8S.fasta.gz
│   └── ERZ12345_*other_ncRNA.fasta.gz
├── functional-annotation
├── pathways-and-systems
└── annotation-summary

Output files

ERZ12345_SSU.fasta.gz: This fasta file contains all sequences from the assembly’s contigs that matched the SSU (Small Subunit) rRNA marker gene. This file may be absent if no marker genes of this type were detected in the assembly.
ERZ12345_LSU.fasta.gz: This fasta file contains sequences matching the LSU (Large Subunit) rRNA marker gene. This file may be absent if no marker genes of this type were detected in the assembly.
*rRNA_bacteria*.fasta.gz: This fasta file contains extracted bacterial rRNA sequences. It may be absent if no bacterial rRNA sequences were detected in the assembly.
*rRNA_archaea*.fasta.gz: This fasta file contains extracted archaeal rRNA sequences. It may be absent if no archaeal rRNA sequences were detected in the assembly.
*rRNA_eukarya*.fasta.gz: This fasta file contains extracted eukaryotic rRNA sequences. It may be absent if no eukaryotic rRNA sequences were detected in the assembly.
*5S.fasta.gz: This fasta file contains extracted 5S rRNA sequences. It may be absent if no 5S rRNA sequences were detected in the assembly.
*5_8S.fasta.gz: This fasta file contains extracted 5.8S rRNA sequences. It may be absent if no 5.8S rRNA sequences were detected in the assembly.
*other_ncRNA.fasta.gz: This fasta file contains extracted non-coding RNA sequences that do not belong to the categories above. It may be absent if no matching ncRNA sequences were detected in the assembly.

These sequences should be interpreted with caution: rRNA genes can be difficult to assemble, for example because of repeats and their high copy number. Their presence, absence, or apparent taxonomic signal should therefore not be used alone to draw definitive conclusions about the assembly or its organisms.

functional-annotation

The functional-annotation directory contains seven subdirectories of results, one for each functional annotation tool used in the pipeline. Specifically, the functional annotations in this directory are assigned on a per-protein basis, and range from tools like InterProScan to run_dbCAN.

├── qc
├── cds
├── taxonomy
├── rnas
├── functional-annotation
│   ├── interpro
│   │   ├── ERZ12345_interproscan.tsv.gz
│   │   ├── ERZ12345_interpro_summary.tsv.gz
│   │   └── ERZ12345_interpro_summary.tsv.gz.gzi
│   ├── pfam
│   │   ├── ERZ12345_pfam_summary.tsv.gz
│   │   └── ERZ12345_pfam_summary.tsv.gz.gzi
│   ├── go
│   │   ├── ERZ12345_go_summary.tsv.gz
│   │   ├── ERZ12345_go_summary.tsv.gz.gzi
│   │   ├── ERZ12345_goslim_summary.tsv.gz
│   │   └── ERZ12345_goslim_summary.tsv.gz.gzi
│   ├── eggnog
│   │   ├── ERZ12345_emapper_seed_orthologs.tsv.gz
│   │   └── ERZ12345_emapper_annotations.tsv.gz
│   ├── kegg
│   │   ├── ERZ12345_ko_summary.tsv.gz
│   │   └── ERZ12345_ko_summary.tsv.gz.gzi
│   ├── rhea-reactions
│   │   ├── ERZ12345_proteins2rhea.tsv.gz
│   │   └── ERZ12345_proteins2rhea.tsv.gz.gzi
│   └── dbcan
│       ├── ERZ12345_dbcan_cgc.gff.gz
│       ├── ERZ12345_dbcan_standard_out.tsv.gz
│       ├── ERZ12345_dbcan_overview.tsv.gz
│       ├── ERZ12345_dbcan_sub_hmm.tsv.gz
│       └── ERZ12345_dbcan_substrates.tsv.gz
├── pathways-and-systems
└── annotation-summary

Output files - interproscan

This subdirectory contains the output generated by running InterProScan on the protein sequences of the assembly.

ERZ12345_interproscan.tsv.gz: This tsv file contains the detailed results from InterProScan, including the InterPro identifiers, descriptions of the functional domains or protein families detected, and the specific proteins from the assembly that match each signature. Each entry links a protein to its associated functional features, such as protein families, motifs, domains, pathway annotations, and Gene Ontology (GO) terms. In this pipeline, InterProScan is run with --iprlookup --goterms --pathways, so the TSV output includes the following columns:
1. Protein accession
2. Sequence MD5 digest
3. Sequence length
4. Analysis. In this pipeline the values come from the configured InterProScan applications: TIGRFAM, SFLD, SUPERFAMILY, GENE3D, HAMAP, COILS, CDD, PRINTS, PIRSF, PROSITEPROFILES, PROSITEPATTERNS, PFAM, MOBIDBLITE, and SMART. SIGNALP is also included when params.interpro_licensed_software is enabled.
5. Signature accession
6. Signature description
7. Start location
8. Stop location
9. Score, which is the e-value or score reported by the member database method
10. Status, indicating the match status
11. Date, indicating the date of the run
12. InterPro annotations accession
13. InterPro annotations description
14. GO annotations with their source(s)
15. Pathway annotations
Further details are available in the InterProScan TSV output format documentation.
ERZ12345_interpro_summary.tsv.gz: This tsv file provides a summary of the count of different InterPro signatures that were detected across all proteins in the assembly. The summary includes the total number of proteins annotated with each InterPro signature, offering a high-level overview of the functional diversity present in the assembly.
ERZ12345_interpro_summary.tsv.gz.gzi: This file is an index for the InterPro count summary file.

Output files - pfam

This subdirectory contains summaries of Pfam domain matches extracted from the InterProScan results.

ERZ12345_pfam_summary.tsv.gz: This tsv file contains a summary of the counts of the different Pfam signatures identified across all proteins in the assembly. Each entry represents a specific Pfam family or domain, with associated counts indicating how many proteins in the assembly match the signature.
ERZ12345_pfam_summary.tsv.gz.gzi: This file is an index for the Pfam count summary file.

Output files - go

This subdirectory contains output files summarising Gene Ontology (GO) annotations extracted from the InterProScan results. In addition to the full set of GO terms, the annotations are also mapped to the metagenomics GO-slim subset (see here) to provide a more concise and domain-specific overview.

ERZ12345_go_summary.tsv.gz: This tsv file contains summary counts of the full set of GO terms assigned to proteins in the assembly.
ERZ12345_go_summary.tsv.gz.gzi: This file is an index for the GO summary count file.
ERZ12345_goslim_summary.tsv.gz: This tsv file contains summary counts of the GO-slim terms (a simplified subset of GO terms) assigned to proteins in the assembly.
ERZ12345_goslim_summary.tsv.gz.gzi: This file is an index for the GO-slim summary count file.

Output files - eggnog-mapper

This subdirectory contains the output of running EggNOG-mapper on the protein sequences from the assembly.

ERZ12345_emapper_seed_orthologs.tsv.gz: This tsv file lists the seed orthologs identified for each protein during the EggNOG-mapper run.
ERZ12345_emapper_annotations.tsv.gz: This tsv file contains the functional annotations assigned to the proteins by EggNOG-mapper using the seed orthologs.

Output files - kegg

This subdirectory contains the results of identifying KEGG Orthologs (KOs) in the assembly’s proteins using hmmsearch, with their occurrences summarised in a count table.

ERZ12345_ko_summary.tsv.gz: This tsv file listing the counts of each KO detected in the assembly.
ERZ12345_ko_summary.tsv.gz.gzi: This file is an index for the KO summary count file.

Output files - rhea-reactions

This subdirectory contains results from running DIAMOND to match the assembly’s proteins against a UniRef90 database with Rhea reactions and corresponding ChEBI compounds assigned.

ERZ12345_proteins2rhea.tsv.gz: This tsv file listing the Rhea reaction IDs and corresponding ChEBI compounds assigned to the proteins in the assembly based on their matches to UniRef90 database.
ERZ12345_proteins2rhea.tsv.gz.gzi: This file is an index for the Proteins2Rhea output.

Output files - dbcan

This subdirectory contains the output of running run_dbCAN on the assembly proteins, generating annotations for CAZymes and CAZyme Gene Clusters (CGC).

ERZ12345_dbcan_cgc.gff.gz: This gff file is annotated with functional genes for CGCFinder and visualization tools.
ERZ12345_dbcan_standard_out.tsv.gz: This tsv file lists all identified CGCs and their components.
ERZ12345_dbcan_overview.tsv.gz: This tsv file contains a summary of identified CAZymes.
ERZ12345_dbcan_sub_hmm.tsv.gz: This tsv file contains the detailed sub-HMMER results.
ERZ12345_dbcan_substrates.tsv.gz: This tsv file contains the substrate prediction results for CGCs.

pathways-and-systems

The pathways-and-systems directory contains five subdirectories of results, one for each pathway/system annotation tool used by the pipeline. The results range from KEGG pathways, to Biosynthetic Gene Clusters (BGCs) detected by antiSMASH and SanntiS. Just like the functional annotations, most of these annotations are on a per-protein basis.

├── qc
├── cds
├── taxonomy
├── rnas
├── functional-annotation
├── pathways-and-systems
│   ├── antismash
│   │   ├── ERZ12345_antismash.gbk.gz
│   │   ├── ERZ12345_antismash.gff.gz
│   │   ├── ERZ12345_merged.json
│   │   ├── ERZ12345_antismash_summary.tsv.gz
│   │   └── ERZ12345_antismash_summary.tsv.gz.gzi
│   ├── sanntis
│   │   ├── ERZ12345_sanntis.gff.gz
│   │   ├── ERZ12345_sanntis_summary.tsv.gz
│   │   └── ERZ12345_sanntis_summary.tsv.gz.gzi
│   ├── genome-properties
│   │   ├── ERZ12345_gp.json.gz
│   │   ├── ERZ12345_gp.tsv.gz
│   │   └── ERZ12345_gp.txt.gz
│   ├── kegg-modules
│   │   ├── ERZ12345_kegg_modules_per_contigs.tsv.gz
│   │   ├── ERZ12345_kegg_modules_per_contigs.tsv.gz.gzi
│   │   ├── ERZ12345_kegg_modules_summary.tsv.gz
│   │   └── ERZ12345_kegg_modules_summary.tsv.gz.gzi
│   └── dram-distill
│       ├── ERZ12345_dram.tsv.gz
│       ├── ERZ12345_dram.html.gz
│       ├── ERZ12345_genome_stats.tsv.gz
│       └── ERZ12345_metabolism_summary.xlsx.gz
└── annotation-summary

Output files - antismash

This subdirectory contains the results of running antiSMASH on the assembly’s proteins, including annotations for detected BGCs in various formats.

ERZ12345_antismash.gbk.gz: A GenBank format file containing antiSMASH annotations.
ERZ12345_antismash.gff.gz: A GFF3 format file containing antiSMASH annotations.
ERZ12345_merged.json: A JSON file containing antiSMASH annotations.
ERZ12345_antismash_summary.tsv.gz: This tsv file listing the counts of each antiSMASH entry detected in the assembly.
ERZ12345_antismash_summary.tsv.gz.gzi: This is the index of the antiSMASH summary tsv

Output files - sanntis

This subdirectory contains the outputs of running SanntiS on the proteins of the assembly, also describing the detected BGCs using this new machine learning-based tool.

ERZ12345_sanntis.gff.gz: This gff file contains the different SanntiS annotations in the GFF3 format. The GFF3 specification can be found in the tool repo
ERZ12345_sanntis_summary.tsv.gz: This tsv file listing the counts of each SanntiS entry detected in the assembly.
ERZ12345_sanntis_summary.tsv.gz.gzi: This is the index of the SanntiS summary tsv

Output files - genome-properties

This subdirectory contains the outputs of running Genome Properties on the proteins of the assembly. Genome properties is an annotation system whereby functional attributes can be assigned to an assembly, based on the presence of a defined set of protein signatures within that assembly. The results are available in three different formats.

ERZ12345_gp.json.gz: A JSON format file containing Genome Properties annotations
ERZ12345_gp.tsv.gz: A tsv file containing Genome Properties annotations in a tab-separated format.
ERZ12345_gp.txt.gz: A plain text file containing the Genome Properties annotations.

Output files - kegg-modules

This subdirectory contains results from evaluating which KEGG modules and pathways are represented in the assembly based on the presence of KEGG Orthologs (KOs). For each module, a completeness score is calculated depending on how many required KOs are detected using the kegg-pathways-completeness-tool.

ERZ12345_kegg_modules_per_contigs.tsv.gz: This tsv file contains the different KEGG modules and their completeness, including the contig they were found on.
ERZ12345_kegg_modules_per_contigs.tsv.gz.gzi: This file is an index for the per-contig KEGG modules file.
ERZ12345_kegg_modules_summary.tsv.gz: This tsv file contains a summary of the KEGG modules and their completeness for the whole assembly, not on a per-contig basis.
ERZ12345_kegg_modules_summary.tsv.gz.gzi: This file is an index for the summary KEGG modules file.

Output files - dram-distill

This subdirectory contains the outputs of running DRAM-distill on the KO hits per contig, the InterProScan and run_dbCan. DRAM generates summary reports and visualisations for the annotations on a per-assembly basis, and outputs four different files.

ERZ12345_dram.tsv.gz: This tsv file contains the product of https://github.com/WrightonLabCSU/DRAM for the assembly, including functions that were detected.
ERZ12345_dram.html.gz: This html file contains a heatmap visualisation of the detected functions by https://github.com/WrightonLabCSU/DRAM.
ERZ12345_genome_stats.tsv.gz: This tsv file contains the genome statistics summary generated by DRAM.
ERZ12345_metabolism_summary.xlsx.gz: This Excel file contains the metabolism summary generated by DRAM.

annotation-summary

The annotation-summary directory contains a single GFF file that summarises the annotations generated by the pipeline, integrating functional annotation per protein and other genomic features. This file is compressed and indexed with both a bgzip index and a tabix index (.gff.gz, .gff.gz.gzi, .gff.gz.csi files respectively).

├── qc
├── cds
├── taxonomy
├── rnas
├── functional-annotation
├── pathways-and-systems
└── annotation-summary
    ├── ERZ12345_annotation_summary.gff.gz
    ├── ERZ12345_annotation_summary.gff.gz.gzi
    └── ERZ12345_annotation_summary.gff.gz.csi

Output files

ERZ12345_annotation_summary.gff.gz: This gff file contains an expansive and large summary of most of the functional annotations each protein has into a single GFF3 format file.
ERZ12345_annotation_summary.gff.gz.gzi: This file is the bgzip index for the annotation summary GFF file.
ERZ12345_annotation_summary.gff.gz.csi: This file is the tabix (CSI) index for the annotation summary GFF file.
ERZ12345_gff_validation_errors.log: If the GFF file is not valid, then a log file is created with the validation errors. This file is not created when the GFF file is valid.

See the assembly analysis pipeline repository for detailed pipeline documentation.

Citation

BibTeX citation:

@online{2026,
  author = {, MGnify},
  title = {Assembly Annotation Pipeline},
  date = {2026-10-15},
  url = {https://docs.mgnify.org/src/docs/analysis/version6/assembly-annotation.html},
  langid = {en}
}

For attribution, please cite this work as:

MGnify. 2026. “Assembly Annotation Pipeline.” October 15. https://docs.mgnify.org/src/docs/analysis/version6/assembly-annotation.html.