When you quality trim sequences in Geneious you can chose to either annotate the trimmed regions (soft trimming) or remove them from the sequence (hard trimming). In the case of soft trims, the sequence will remain but will be annotated with a pink “Trimmed” annotation, and will be ignored by many tools such as the assembler. This means soft trims can be adjusted as needed, or deleted completely. Soft trims can be confusing to users of other software because the sequence is visible in the assembly but is not contributing to the assembly and won’t be part of the consensus sequence. Dragging the ends of the trim annotation will make the newly untrimmed sequence visible and part of the consensus.
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