Barrnap

tRNAscan-SE is a tool for detecting transfer RNA genes in genomic or metagenomic sequences. In this module, it predicts bacterial tRNA genes from an assembly FASTA file and summarizes tRNA classes, pseudogenes, introns, and total tRNA length.

Workflow

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

2. Run bacterial tRNA prediction
   Use tRNAscan-SE in bacterial mode to identify tRNA genes from the input sequences.

3. Generate annotation and sequence files
   Export predicted tRNA results, secondary structure files, statistics, BED/GFF annotations, FASTA sequences, and isotype information.

4. Summarize tRNA results
   Report total tRNAs, standard tRNAs, special tRNA classes, predicted pseudogenes, intron-containing tRNAs, and total tRNA length.

Data

The Barrnap sample dataset uses the assembled metagenomic FASTA file from sample ERR260162, such as ERR260162.scaffold_500bp.fa or ERR260162.scaftig.fa. This dataset demonstrates bacterial rRNA prediction from assembled metagenomic sequences and generation of rRNA annotation and FASTA output files.

Result

v0.1: The pipeline is stored in Code Repository: CRS1241439613135106048. The computational docker enrionment is stored in Software Repository: SRS1241446578691256320.

Reproducibility

The pipeline utilizes code CRS1241439613135106048 and Docker image SRS1241446578691256320, both of which are stored in the BMAP repositories.

Usage

1. Select the application 'tRNA-SE bacterial analysis'
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.