Question

What is the difference between gbk and gbf file?

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3.9 years ago

traditionalGuy ▴ 60

prokka 1.13.7 is generating gbf file instead of gbk. They look similar. Is there any difference?

annotation prokka • 7.7k views

ADD COMMENT • link updated 3.1 years ago by oschwengers ▴ 120 • written 3.9 years ago by traditionalGuy ▴ 60

score 1 · Answer 1 · 2021-02-13

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3.9 years ago

Arsenal ▴ 160

Gbk format is outdated. Gbf replaced it some time (years) ago. From the NCBI Genomes Download (FTP) FAQ:

GenBank flat file format of the genomic sequence(s) in the assembly. This file includes both the genomic sequence and the CONTIG description (for CON records), hence, it replaces both the .gbk .gbs format files that were provided in the old genomes FTP directories.

ADD COMMENT • link 3.9 years ago by Arsenal ▴ 160

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If gbk format is outdated, why is my Prokka’s version 1.14.5 deleting unwanted file .gbf and changed it to .gbk? Thanks.

ADD REPLY • link 3.1 years ago by neokao • 0

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For some reason NCBI's tbl2asn tool (which Prokka uses to create to GenBank files) writes wrong COORDINATES inference tags. Thus, Prokka fixes this and writes corrected Gbk files -> prokka#L1419

ADD REPLY • link 3.1 years ago by oschwengers ▴ 120