Sequence Trimming

Sequence Trimming

Automated DNA sequencers occasionally produce poor quality reads, particularly near the sequencing primer site, and toward the end of longer sequence runs. The sequences of clones from DNA libraries frequently contain vector sequence, polyA tails, or other unrelated sequence. Introns and primer sequence frequently flank the sequence of amplified exons. Unless removed by trimming, any of these artifacts will distort your sequence assembly and downstream sequence analysis.

Sequencher provides simple-to-use but powerful tools that help you trim poor quality or ambiguous data:

Trim Ends removes misleading data from the ends of sequencing fragments.

Trim Vector removes sequence-specific data contaminating the ends of your sequences.

Trim to Reference eliminates the ends of sequences that extend beyond an assembled Reference sequence.


Prior to executing a trim, Sequencher displays a graphic representation of the proposed trim, which allows you to even further refine your criteria.


If you want to restore a set number of bases on either or both ends of your trimmed sequences because your trim was too stringent or you want to improve coverage, Batch Revert Trim Ends lets you do just that. With just a few clicks, you can restore bases to just a few or a few thousand sequences, and get even more control over your sequence trims.

Check out the Trimming Tutorial to learn how to take advantage of these tools. The Quality Scores Tutorial expands on the use of confidence scores in trimming and navigating your sequences.