Developer: SoftGenetics, LLC
Supported platforms: Windows (v5.2.0 referenced in vendor materials; macOS supported only via virtualization or Boot Camp on Intel Macs)
Download: https://www.softgenetics.com/products/mutation-surveyor/
Features
View Quality scores
Yes. Displays Phred quality scores and applies configurable Signal-to-Noise and Quality Score trimming thresholds across paired bidirectional reads.
View raw data
Yes. Project settings include an option to select raw trace data instead of processed trace data (alongside a Raw Data to Processed Data command), and the Output Trace Data tool exports frame-by-frame trace intensities to tab-delimited text.
Assembly
Yes. Uses patented physical trace anti-correlation alignment against reference traces or synthetic/GenBank references (plus a Sequence Assembly tool to merge traces into reference sequences).
Input file formats
.ab1, .abi, .scf, .gz, .esd, and .rsd trace files, plus GenBank (.gbk, .gb), FASTA, and .seq references (also accepts CEQ and Promega Spectrum traces).
Output file formats
.scf, .vcf, .txt, .xls/.xlsx, .xml, .htm, HGVS nomenclature tables, and direct Word image/report export.
Trimming
Yes. Five layered trimming modes (Quality S/N trim, Score trim, fixed 5′/3′ trim, and vector trim/masking).
Integrated Blast
No interactive NCBI BLAST client inside the trace viewer (queries SoftGenetics’ internal GenBank reference database automatically instead).
Open multiple windows
Yes, including synchronised 1D/2D forward/reverse chromatogram comparison panes, mutation tables, and annotation browsers.
Edit bases
Yes. Reference and sample base calls can be edited through Edit Base; modified traces can be saved separately and reprocessed.
ABI limits (regions outside of clear range region are displayed in gray)
Import and display of instrument ABI clear-range tags is not confirmed; Mutation Surveyor provides its own multi-rule Quality and Score trim cutoffs.
Other functions
- Low-level somatic/mosaic variant sensitivity down to ~5% of the primary peak
- Automated heterozygous indel deconvolution, DNA methylation analysis, and mitochondrial rCRS D-loop alignment
- High throughput—processes up to 2,000 trace files in under 15 minutes with ClinVar/dbSNP/gnomAD track support
Cost
Paid Windows software with a 35-day full-feature trial. Published single-machine annual subscriptions are $1,900 USD for academic/government users and $3,800 USD for corporate users; contact SoftGenetics for network, perpetual, or educational licensing.
Comments
Mutation Surveyor is built specifically for clinical genetics, somatic/low-frequency SNP detection, and validated high-throughput Sanger variant calling rather than general plasmid cloning. Its physical electropherogram comparison and raw-trace inspection options give it a distinct edge for diagnostic laboratories.
Return to the Trace Viewers overview or check trace quality online with QualTrace III Online.