What is the difference between gbk and gbf file?
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11 months ago

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

annotation prokka • 1.3k views
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11 months 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Gbk format is outdated.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.

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If gbk format is outdated, why is my Prokka’s version 1.14.5 deleting unwanted file .gbf and changed it to .gbk?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

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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

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