EMBL2checklists

EMBL2checklists converts EMBL or GenBank flat files of plant and fungal DNA barcoding sequences into marker-specific ENA submission checklists for deposition to the European Nucleotide Archive via the Webin system.

Key Features:

• Automation and conversion: Converts sequences, annotations, and metadata into marker-specific ENA checklist formats in an automated process.
• Input format support: Accepts EMBL and GenBank flat file formats as input.
• Annotation and metadata integration: Integrates sequence annotations and sample metadata into the generated checklists.
• Output format: Produces tab-delimited spreadsheets that conform to ENA checklist requirements and are ready for upload via Webin.
• Implementation: Implemented as a Python package operable across platforms.
• Post-processing: Generates editable checklist files for modification after conversion.

Scientific Applications:

• Plant phylogenetics: Facilitates submission of plant DNA barcoding sequences to ENA to support phylogenetic and biodiversity studies.
• Fungal metagenomics: Facilitates submission of fungal DNA barcoding sequences from metagenomic investigations to ENA for data sharing and downstream analyses.

Methodology:

Converts input files from EMBL or GenBank formats into tab-delimited spreadsheets that conform to ENA checklist requirements by extracting sequence annotations and metadata and producing marker-specific checklists ready for upload via the Webin submission system.