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nigyta / dfast_core

DDBJ Fast Annotation and Submission Tool
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Genbank-output: circular-tag #45

Open xJane01x opened 1 year ago

xJane01x commented 1 year ago

Hallo,

very useful and fast annotation tool!

How can I add the circular tag for complete chromosomes and plasmids in the genbank file instead of editing manually? Is there any option?

completness and topology are part of the fasta-identifier in the input files.

Thanks for your help.

nigyta commented 1 year ago

Yes, you can add them with --complete t, --seq_names, --seq_topologies, --seq_types options.

Here is a minimum example:

dfast -g example/sample.lactobacillus.fna --complete t  --seq_names "Chromosome,pXXXX,pYYYY" --seq_topologies c,c,l --seq_types c,p,p --no_cdd --no_hmm --no_cds --no_rrna --no_trna --no_crispr --force

In this example, the input genome consists of 1 circular chromosome (Chromosome), 1 circular plasmid (pXXXX), 1 linear plasmid (pYYY).

Please see the document below for more detail: https://github.com/nigyta/dfast_core/blob/master/docs/insdc_submission.md#for-a-complete-genome