Developer: Gene Codes Corporation
Supported platforms: Windows and legacy macOS (32-bit; 64-bit macOS build in beta)
Download: https://www.genecodes.com/
Features
View Quality scores
Yes. Reads confidence values from ABI/KB, SCF, PHD, QUAL, and FASTQ files and color-highlights bases by confidence threshold.
View raw data
Yes (toggleable chromatogram inspection alongside aligned contigs, with non-destructive revert to experimental data).
Assembly
Yes. Industry-standard de novo and reference-guided Sanger contig assembly, “Assemble by Name” batch grouping, and NGS connections (Velvet, BWA, GSNAP).
Input file formats
ABI (.ab1), SCF, MegaBACE, CEQ, ALF, FASTA, FASTQ, GenBank, EMBL, DDBJ, PHD, and SEQ.
Output file formats
FASTA, GenBank, SCF, CAF/SPF project assemblies, VCF (via SAMtools), and summary variance reports.
Trimming
Yes. Non-destructive quality, ambiguity (N), vector (VecBase), and reference end trimming with graphical preview and batch revert.
Integrated Blast
Yes (submits sequences or consensus contigs directly to NCBI BLAST or local BLAST; direct queries capped at 7,800 bp on macOS / 1,600 bp on Windows).
Open multiple windows
Yes, with synchronized contig, overview, and chromatogram windows.
Edit bases
Yes, with auditability and instant revert to original experimental calls.
ABI limits (regions outside of clear range region are displayed in gray)
Uses non-destructive internal trim markers rather than ABI clear-range shading.
Other functions
- Global and local secondary-peak detection with Variance Tables for SNP and heterozygote review
- Multi-frame translations, restriction mapping, and reusable project templates
- Sequencher Connections wrappers for FastQC, MUSCLE, SAMtools, Cufflinks, and Tablet
Cost
Paid (quote-based standalone and network licenses, including 1 year of support/upgrades; free demo mode available).
Comments
Sequencher has been a gold-standard commercial contig assembly and mutation-proofreading tool in core facilities and clinical labs for decades. Prospective Mac users on modern macOS releases should confirm 64-bit compatibility with Gene Codes before purchasing.
Return to the Trace Viewers overview or check trace quality online with QualTrace III Online.