PEPPAN takes GFF3 files as input. You can use a single GFF3 file if the file contains nucleotide sequences at the end of the file, or append a separate file of nucleotide sequences after the GFF file. Both files can either be in plain text or in GZIP format.
GFF3 files generated by Prokka can directly be used as input for PEPPAN without modification.
GFF3 files from GenBank or RefSeq only contain annotation and no nucleotide sequences. Thus, a separate file of nucleotide sequences needs to be added in addition to the GFF3 file, with a comma separating the two files. For example, use
GCF_000006785.2_ASM678v2_genomic.gff.gz,GCF_000006785.2_ASM678v2_genomic.fna.gz
as input for the Streptococcus pyogenes M1 GAS genome.
Note: you do not need to modify either of these two files because PEPPAN uses the GZIPped files by default.