Prokaryotic annotation

An annotation pipeline for bacterial genomes

Quick Start

To execute the pipeline on your computer, first pull the docker image

docker pull hadrieng/prokka

Then execute the workflow

nextflow run annotation.nf --genome $path_to_your_genome

It will produce an embl file ready for submission (given you have registered a bioproject and locus tag) as well as .gbk, .gff and other files from the output of prokka

Pipeline Parameters

--genome

• Specifies the location of the genome fasta file
• Required

--bioproject

• The Bioproject you registered at ENA
• If not set, will be PRJEBXXXXX

--genus

• The genus of the genome to annotate

--species

• the species of the genome to annotate

--strain

• the strain of the genome to annotate

--locus_tag

• The desired locus tag. Should also be registered at ENA
• If not set, it will be XXX

--taxonomy

• the taxid of your organism

Profiles

The SGBC cluster uses a module system. Pulling the docker image is not required!

By default, the pipeline runs locally using docker. If you run the annotation pipeline on the SGBC cluster, please pass the option -profile planet

Example:

netxflow run annotation.nf -profile planet --genome data/aureus.fasta \
--bioproject PRJEB12345 --genus Staphylococcus --species aureus \
--strain ST250_MRSA-1 --locus_tag SA0 --taxonomy 1280

Citations

If you use this pipeline in your research, please cite:

• Circlator: automated circularization of genome assemblies using long sequencing reads, Hunt et al, Genome Biology 2015 Dec 29;16(1):294. doi: 10.1186/s13059-015-0849-0. PMID: 26714481.
• Seemann T. Prokka: rapid prokaryotic genome annotation, Bioinformatics 2014 Jul 15;30(14):2068-9. PMID:24642063
• GFF3toEMBL: Preparing annotated assemblies for submission to EMBL", Andrew J. Page, Sascha Steinbiss, Ben Taylor, Torsten Seemann, Jacqueline A. Keane, The Journal of Open Source Software, 1 (6) 2016. http://dx.doi.org/10.21105/joss.00080