nds / mettannotator

METT annotation

Introduction

ebi-metagenomics/mettannotator is a bioinformatics pipeline use to annotate assemblies using the following tools:

Tool/Database	Version	Purpose
Prokka	1.14.6	Protein annotation
eggNOG-mapper	2.1.11	Protein annotation (eggNOG, KEGG, COG, CAZy)
eggNOG DB	5.0	Database for eggNOG-mapper
Diamond	2.0.11	Protein annotation (eggNOG)
InterProScan	5.62-94.0	Protein annotation (InterPro, Pfam)
CRISPRCasFinder	4.3.2	Annotation of CRISPR arrays
AMRFinderPlus	3.11.4	Antimicrobial resistance gene annotation; virulence factors, biocide, heat, acid, and metal resistance gene annotation
AMRFinderPlus DB	3.11 2023-02-23.1	Database for AMRFinderPlus
SanntiS	0.9.3.2	Biosynthetic gene cluster annotation
Infernal	1.1.4	RNA predictions
tRNAscan-SE	2.0.9	tRNA predictions
Rfam	14.9	Identification of SSU/LSU rRNA and other ncRNAs
VIRify	-	Viral sequence annotation
MoMofy	1.0.0	Mobilome annotation

Usage

First, prepare a assemblies_sheet with your input data that looks as follows:

assemblies_sheet.csv:

prefix,assembly
BU_ATCC8492VPI0062_NT5002,BU_ATCC8492VPI0062_NT5002.fa
...

Now, you can run the pipeline using:

nextflow run ebi-metagenomics/mettannotator \
   -profile <docker/singularity/...> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

Warning: Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

ebi-metagenomics/mettannotator was originally written by @mberacochea.

We thank the following people for their extensive assistance in the development of this pipeline:

• @KateSakharova
• @tgurbich

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.