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TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission 🧬 💻

PATHOGEN ANNOTATION AND SUBMISSION PIPELINE

Overview

TOSTADAS is a tool designed to fulfill common sequence submission use cases. The tool runs three sub-processes:

1. Metadata Validation – This workflow checks if metadata conforms to NCBI standards and matches the input .fasta file
2. Gene Annotation – This workflow runs gene annotation on input fasta-formatted genomes using one of four sub-workflows: Repeatmasker, Liftoff, VADR or BAKTA
3. Submission – This workflow generates the necessary files and information for submission to SRA. Optionally, you can submit fastq files and metadata without performing gene annotation.

The pipeline execution allows users to choose which sub-workflows and portions of the pipeline to run using various run-time and workflow parameters.