Sequencher

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

Sanger:

• 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. 

NGS:

• 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.

RNA-Seq:

• 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.

New features for Sanger and Next-Generation DNA Sequence Analysis include:

Sanger: 

• New Batch Revert Trim Ends command.
• Ability to adjust the font size in the Project Window.  
• For hybrid sequencing projects, you can create NGS reference databases/indexes directly from the consensus sequences in the Project Window in addition to linking to an external sequence.

NGS:

• GSNAP and BWA-MEM workflows now produce BAM files. 
• Enhancements to the External Data Browser (EDB).  
• FastQC Reports now open automatically.

Gene Codes announces the release of Sequencher 5.4.  This new release adds features to Sanger, NGS and RNA-Seq analyses such as:

• Expanded Cufflinks suite with the addition of Cuffquant and Cuffnorm.  Sequencher 5.4 also has replicates functionality with a unique Conditions and Replicates Editor for Cuffdiff and Cuffnorm.
• Enhanced RNA-Seq visualizations with custom sorting and filtering options.
• 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.
• Updated version of GSNAP which runs faster and has additional alignment modes.
• An updated External Data Browser for organizing both DNA-Seq and RNA-Seq projects.
• Sequencher Connections has improved organization and usability.