Sequencher 5.4.6 is Released!

New and enhanced features for all of your DNA sequence analysis.


  • Send primer pair sequences from Primer-BLAST runs in Sequencher Connections to your Sequencher project.
  • Easily use consensus sequences from the Project Window as a reference sequence for NGS alignments for hybrid sequencing projects.
  • New Batch Revert Trim Ends command.
  • Ability to adjust the font size in the Project Window. 


  • Faster GSNAP and BWA-MEM workflows.
  • Build GSNAP Databases and BWA Indexes that can be re-used for aligning to whole genomes.
  • View and save quality scores and metadata of your NGS raw data files with FastQC reports.
  • Generate Variant Calling Files (VCF) to flag variants in your NGS alignments using SAMtools.


  • Expanded Cufflinks suite with the addition of Cuffquant and Cuffnorm.
  • A unique Conditions and Replicates Editor for Cuffdiff and Cuffnorm.
  • Enhanced RNA-Seq visualizations with custom sorting and filtering options.   
  • Easily manage all of your DNA-Seq and RNA-Seq projects with an enhanced External Data Browser.