November 14, 2017   |   Technical note

Arkgene Microbial Automated Annotation Pipeline

Looking for a faster and hassle-free way to annotate your bacterial genome?

Automated Microbial Genome Annotation Pipeline includes a list of software to annotate assembled microbial genome. This pipeline starts with the two softwares used to predict rRNA and tRNA genes, respectively. After the predictions, the genome will be masked with the predicted rRNA and tRNA sequences. Next, the masked genome will be subjected to gene prediction using Prodigal software. The predicted gene model will be annotated with gene identity by BLAST (DIAMOND BLASTP) searching against microbial genomes extracted from UniProt Protein Database.

Step 1 : Click “Applications” on the left panel, click on “Microbial Workbench”.
Step 2 : Click “Optimised Pipelines” from the panel.
Step 3 : Click “Go” on Mirobial Annotation, you will redirect to the Microbial Annotation file selection page.
Step 4 : Click “Select File”, select supported file type. Select the input file and click “Select”.
(currently, only fasta file with .fa and .fna is supported with a maximum file size of 10 MB).
Step 5 : Click dropdown menu for “EVALUE”. The EVALUE is for the DIAMOND BLASTP parameter.
Step 6 : Enter “Output Name”. No space are allowed.
Step 7 : Click “Go” to execute the pipeline.

Output results can be imported to or CGBASE and ClicO for visualisation. A notification of the job is running will be appear on the upper right corner under the notification bell. To see a list of running jobs, click on “My Jobs”, the status of the job will be shown here together with the CPU (units) consumed. All completed jobs will be appeared in the “Analysis Results” page with the prefix of the type of job and the date of the job being executed.

How fast is our microbial genome annotation pipeline? Here are some stats for reference: