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