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Updated docs.
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rfm-targa committed Feb 22, 2024
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Expand Up @@ -11,7 +11,7 @@ Important Notes
We strongly recommend using the same Prodigal training file for schema creation and allele calling to ensure consistent results.
- chewBBACA defines an allele as a complete Coding DNA Sequence (CDS), with start and stop codons
according to the `NCBI genetic code table 11 <http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi>`_
(identified using `Prodigal <https://github.com/hyattpd/prodigal/releases/>`_ for chewBBACA>=3.2.0 and
(identified using `Prodigal <https://github.com/hyattpd/prodigal/releases/>`_ for chewBBACA<=3.2.0 and
`Pyrodigal <https://github.com/althonos/pyrodigal>`_ for chewBBACA>=3.3.0, but with the option to provide FASTA
files with CDSs). It will automatically exclude any allele for which the DNA sequence does not contain start or stop
codons and for which the length is not multiple of three. Alleles that contain ambiguous bases are also excluded.
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