gbk2tbl

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Overview

This command converts a GenBank file (with a .gbk or .gb extension) into a feature table (.tbl) and generates a corresponding FASTA file (.fsa). These outputs are necessary for downstream processing with tools like table2asn.

You would generally want to use this when you get Genbank flatfiles (.gbk) from external tools like phold.

Warning

For now, it is not recommended to use the phold GenBank file as it contains features that are not compatible with NCBI GenBank.

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Required Input

• -i, --input: Input GenBank file. (Required)

Optional Parameters

• -m, --mincontigsize: Minimum contig size to process (default: 0).

• -p, --prefix: Prefix for output filenames (default: “seq”).

Output

• <prefix>.fsa: FASTA file containing the sequence(s).

• <prefix>.tbl: Feature table for GenBank submissions.

Example Usage

suvtk gbk2tbl -i annotation.gbk -p myprefix