How to run genomad on only complete sequences (DTR or ITR)?

[ZongzhiWu]

How to run genomad on only complete sequences (DTR or ITR), but not on fragments.

[apcamargo]

You can filter those using the topology column of the summary file. If you want to process only the punitively complete genomes, you'd need to filter fragments before running geNomad. If you are comfortable with Python, you can use the Sequence class within geNomad to achieve that. It has properties that indicate whether a sequence has DTRs or ITRs (see here).