Developer: Benchling, Inc.
Supported platforms: Web browser (Windows, macOS, Linux, ChromeOS)
Access: https://www.benchling.com/
Features
View Quality scores
Yes. Light grey bars behind chromatogram peaks display trace quality scores on hover, alongside optional quality-based base capitalisation.
View raw data
Displays four-colour processed electropherogram peaks aligned beneath base calls; does not expose unprocessed capillary voltage or sensor channels.
Assembly
Multi-sequence alignment and trace-quality-weighted consensus generation using MAFFT v7 (pairwise, multi-sequence, or consensus alignments against templates; high-throughput Sanger batch workflows are available on enterprise PipeBio add-ons).
Input file formats
Sequence import supports .ab1, .scf, .ape, .dna (SnapGene), .fasta, .gb, .seq, .xdna, .cm5, and .zip; DNA alignment uploads accept .ab1, .ftv, .fasta, .gb, and .geneious.
Output file formats
Consensus DNA sequences stored in cloud projects, alignment exports, GenBank/FASTA exports, and download of original uploaded .ab1 trace files.
Trimming
Manual read trimming via draggable black trim handles or right-click Trim… controls (trimmed regions grey out and are excluded upon realignment).
Integrated Blast
Yes—Benchling BLAST searches DNA and amino-acid sequences within Benchling. This is distinct from searching NCBI’s public databases.
Open multiple windows
Yes, via multiple browser tabs and split-pane sequence/alignment workspace views.
Edit bases
Yes, on derived sequences and consensus outputs (original .ab1 files remain intact).
ABI limits (regions outside of clear range region are displayed in gray)
Import and display of instrument ABI clear-range tags is not confirmed; Benchling provides its own manual greyed-out trim markers on aligned traces.
Other functions
- Cloud electronic lab notebook (ELN) linking sequencing alignments directly to plasmids and cloning records
- Interactive restriction mapping, Golden Gate / Gibson assembly, primer design, and CRISPR guide design
- Trace-quality consensus voting when forward and reverse reads disagree
Cost
Free for individual academic researchers and university teaching labs (includes the Molecular Biology suite and ELN, without Registry/Inventory). Commercial and enterprise tiers are custom quote-based.
Comments
Benchling is one of the most popular cloud platforms for checking Sanger cloning results because you can drag .ab1 traces straight onto a template plasmid and inspect discrepancies with trace-quality bars and automatic reverse-complement alignment in any browser. Labs requiring offline analysis or local trace storage can pair it with desktop tools such as SnapGene or ApE.
Return to the Trace Viewers overview or check trace quality online with QualTrace III Online.