A Free Chromas Alternative That Reads and Assembles Traces in a Browser
SeqBench's Sanger Trace Viewer opens .ab1 and .scf chromatograms in a tab — base calls, per-base Phred and all four dye channels — with no account, nothing to install, and no Windows required.
The difference that matters most is one row down the table: assembling several reads into a contig is what separates free Chromas from paid ChromasPro, and here it is free. Four things Chromas does and this does not are in the table too, rather than left for you to discover.
SeqBench vs Chromas
| Aspect | SeqBench | Chromas / ChromasPro |
|---|---|---|
| Access model | Web app, no account, nothing to install | Windows desktop download |
| Operating system | Any — it is a web page, so macOS and Linux included | Windows (Wine or a VM elsewhere) |
| Price | Free, including the assembly | Chromas is free; ChromasPro is paid |
| ABIF traces (.ab1 / .abi) | Yes — base calls, per-base Phred and all four dye channels | Yes |
| Staden traces (.scf) | Yes — version 2 and version 3 layouts, 1- and 2-byte samples | Yes |
| Assembling several reads | Yes, free, on the viewer page itself — orientation worked out from the overlaps, ends trimmed by quality, and every position the reads disagree on listed | ChromasPro only, which is the paid product |
| Mixed / secondary peaks | Yes — the second base at each position with its minor fraction, plus the bases past the instrument's last call | Yes — mixed bases shown in the trace |
| Comparing a read against a reference | Yes — identity, coverage and every mismatch and indel written in HGVS g. notation | Not in the free viewer |
| A whole plate at once | Yes — a folder or ZIP of reads in, one verdict per clone out, each citing the positions it rests on | No — one trace at a time |
| Editing a base call by hand | Yes — replace, insert, delete, trim or restore any call, with undo/redo; a hand-corrected base carries no Phred score rather than inheriting the machine's, and the edited read downloads as SCF, FASTA or FASTQ or goes straight into the assembly | Yes |
| Re-basecalling the trace | Recovers the tail past the instrument's last call, so usable bases the basecaller stopped short of are read back | Yes, via the paid PeakTrace service |
| Printing a chromatogram | Exports as SVG, PNG or PDF — vector output for a figure, and print from there | Yes, including batch printing |
| Other trace formats | ABIF and SCF; anything else is identified by what it actually is rather than refused generically | Also reads several older instrument formats |
| Exporting the read | Yes — FASTA, plus the trace figure as SVG, PNG or PDF | Yes — FASTA and batch export |
| Where the file goes | Trace decoding, viewing and editing stay in your browser. Assembly, mixed-peak analysis and plate screening send only derived sequence/trace data; reference comparison sends the selected trace for in-memory processing. | On your own PC |
| API and AI-agent access | Yes — the same parsers behind a JSON REST endpoint and an MCP server | No public API |
Comparison is simplified and provided in good faith — check Technelysium for current behavior. Chromas and ChromasPro are products of Technelysium Pty Ltd and are not affiliated with SeqBench.
Where SeqBench is the better fit
- You are on a Mac or Linux, or on a machine you cannot install software on
- You want the forward and reverse reads joined without buying ChromasPro
- You have a plate of clones and want one verdict each, not 96 traces to squint at
- The trace looks mixed and you want the minor fraction at each position
- You want the same parsers from a script or an AI agent
Related Sanger tools
Inspect chromatograms, compare a read with its reference, or screen a whole plate of clones.
No colonies, every clone empty vector, or no PCR band: get the causes your design and your control plates actually implicate, and the cheapest experiment that separates the top two.
Frequently asked questions
Is there a free Chromas alternative for Mac or Linux?
Yes — this one runs in a browser, so the operating system does not come into it. Chromas is a Windows program; the usual answers on a Mac are a virtual machine, Wine, or 4Peaks. SeqBench opens the same .ab1 and .scf files in a tab, parses them locally, and does not ask for an account.
Can I assemble forward and reverse reads without paying for ChromasPro?
Yes. The Sanger Assembly tool takes two or more traces, works out which read is reverse from the overlaps, trims the ends by quality and returns one consensus with the depth at every position. Assembly is the feature that separates free Chromas from paid ChromasPro; here it is free and it is the same page as the viewer.
Does it open .scf files?
Yes, in both the version 2 and version 3 layouts and at either sample width. SCF is what MegaBACE instruments and several European facilities emit, and it is the format most browser trace viewers quietly refuse.
Is my chromatogram uploaded anywhere?
Trace decoding, viewing and editing happen in your browser. Assembly sends derived base calls and quality scores, mixed-peak analysis sends derived dye-channel arrays, and clone screening sends derived reads rather than the facility ZIP. If you choose Compare with a reference, the selected trace is sent to SeqBench for in-memory analysis. None of those inputs is logged or stored.
Which trace formats does it open?
ABIF (.ab1) and SCF, which is what every current Sanger instrument and service returns — including the files your sequencing provider emails you. They open in the browser, so the trace is never uploaded, and the same file can go straight into a reference comparison or a plate verdict rather than only being viewed.
Can I check a whole plate of clones?
Yes — choose Screen clones or a plate on the Sanger Trace Viewer page. Give it a ZIP or a folder of reads and the construct they were supposed to be, and it groups the reads into clones from their file names and returns one verdict per clone, each citing the positions it rests on. Chromas has no equivalent; it reads one trace at a time.
What if the trace is a mixture rather than one clone?
The mixed-peak reader reports the second base at each position with its fraction, which is a measurement of the trace. If you know what the alternatives could be — the intended construct, empty backbone, a double insert — the mixed-trace deconvolution tool fits the read against those molecules and tells you the proportions, plus an R² that says whether the tube holds something you did not list.