Prodigal

Prodigal is a gene prediction tool for identifying protein-coding sequences in microbial and metagenomic assemblies. In this module, Prodigal predicts ORFs from assembled FASTA sequences and exports nucleotide, protein, and annotation files.

Workflow

1. Input assembly FASTA
   Upload assembled scaffold or scaftig sequences in FASTA format.

2. Run metagenomic ORF prediction
   Use Prodigal in metagenomic mode to predict protein-coding genes from the input assembly.

3. Generate raw prediction files
   Export predicted genes as nucleotide sequences, amino acid sequences, and GFF annotation.

4. Filter short ORFs
   Remove predicted ORFs shorter than 100 nt.

5. Summarize gene prediction results
   Report raw ORF count, retained ORF count, total nucleotide length, and total amino acid length.

Data

The Prodigal sample dataset contains an assembled metagenomic FASTA file from sample ERR260162, such as ERR260162.scaffold_500bp.fa or ERR260162.scaftig.fa. This dataset is used to demonstrate metagenomic ORF prediction and generation of predicted gene nucleotide sequences, protein sequences, and GFF annotation files.

Result

v0.1: The pipeline is stored in Code Repository: CRS1240090143516536832. The computational docker enrionment is stored in Software Repository: SRS1240090809144193024.

Reproducibility

The pipeline utilizes code CRS1240090143516536832 and Docker image SRS1240090809144193024, both of which are stored in the BMAP repositories.

Usage

1. Select the application 'Prodigal'
2. Click on the 'Analysis' button
3. Click on the 'Metagenomics pipeline'
4. Fill in the request parameters

5. Upload the compressed data in gz or rar format.