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add annotation summary to readme #88
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oschwengers committed Jan 21, 2022
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Expand Up @@ -255,7 +255,7 @@ Protein sequences provided in short Fasta or GenBank format are searched with de

Annotation results are provided in standard bioinformatics file formats:

- `<prefix>.tsv`: annotations as simple human readble tab separated values
- `<prefix>.tsv`: annotations as simple human readble TSV
- `<prefix>.gff3`: annotations & sequences in GFF3 format
- `<prefix>.gbff`: annotations & sequences in (multi) GenBank format
- `<prefix>.embl`: annotations & sequences in (multi) EMBL format
Expand All @@ -264,6 +264,7 @@ Annotation results are provided in standard bioinformatics file formats:
- `<prefix>.faa`: CDS/sORF amino acid sequences as FASTA
- `<prefix>.hypotheticals.tsv`: further information on hypothetical protein CDS as simple human readble tab separated values
- `<prefix>.hypotheticals.faa`: hypothetical protein CDS amino acid sequences as FASTA
- `<prefix>.txt`: summary as TXT

The `<prefix>` can be set via `--prefix <prefix>`. If no prefix is set, Bakta uses the input file prefix.

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