Problem with the name of Res.fasta and questions about replicons

[HeloiseMuller]

Hi,

Thank you for developping this tool. It is really great to be able to annotate several elements in one command line. After running Bacant v3.4.0 on some genomes I have some comments and questions:

• I suppose this is a typo in the output: annotaion.htlm. And that it should be annotation.htlm?
• I downloaded the last database (v3.1) and when using this database (with the option -p), my outputs for resistance genes were all empty. I realized that in the version 3.1 the files are called Res.fasta.n* instead of Res.n.*. There was no error message though, intead the message said "AMR done", like if it worked fine. Would it be possible to add a checking for the db, in addition of the checking of the fasta file?
• By the way, for replicons, the name of the file is replicon.fasta.n**, which is what is indeed read by bacant (no need to rename it contraty to Res.fasta).
• If I am not mistaken, there is no mention of Replicons in the article Would it be possible to speak about them in the README? Would it be possible to have some information on that? Where does the database come from? What are the blast parameters (since we cannot set -c and -i on those) ? Is there anything else other than the blast done? I was also wondering whether it would be possible in a next version to add the replicons to the annotation.tsv?
• And finally, would you have any advice on how to choose the -c and -i parameters?

Thank you