Sanger Trace Viewer — Read .ab1 Chromatograms
View an .ab1 / .abi Sanger chromatogram, read the base calls and export the trace.
🌐 Nothing you paste is logged or stored — every tool is also callable via REST & MCP, and in bulk from the batch tools
Upload a Sanger sequencing trace (.ab1 / .abi) and read the chromatogram in seconds. SeqBench parses the raw ABIF file and returns the four processed dye channels as an electropherogram — G black, A green, C blue, T red — with the called bases positioned over their peaks. It reports the read length and mean Phred quality, lets you copy or download the base calls as FASTA, and exports the trace figure as SVG or PNG. Your file is used only to produce the trace and is never logged or stored, and the same parsing is available via the REST API and the MCP server.
Nothing you upload is logged or stored.
The viewer decodes the raw ABIF (.ab1 / .abi) chromatogram: the four processed dye channels are drawn as an electropherogram (G black, A green, C blue, T red) with the called bases positioned over their peaks. Read length and mean Phred quality summarise the read; export the base calls as FASTA or the trace as an SVG/PNG figure. Low peaks, broad or overlapping peaks, and stretches of low quality near the ends are the usual signs to trim before downstream analysis.
Working on a whole construct rather than one trace? Open SeqStudio — the full editor, with live feature annotation, plasmid maps, restriction and primer panels, undo/redo, multi-document tabs and GenBank / SnapGene import and export.
How to use the Sanger Trace Viewer tool
- 1Upload your Sanger trace file (.ab1 or .abi) from your sequencer.
- 2Scroll the electropherogram to inspect peak shape and the base calls above each peak.
- 3Check the read length and mean quality, then export the base calls as FASTA or the trace as SVG/PNG.
Frequently asked questions
Which file formats can I open?
ABIF traces from Sanger sequencers — files with an .ab1 or .abi extension. The viewer parses the raw big-endian ABIF directory to extract the base calls (PBAS), per-base quality (PCON), the four processed trace channels (DATA9–12 mapped by FWO_) and the peak locations (PLOC). SCF is not decoded; convert it to .ab1 first.
Is my trace file stored?
No. The .ab1 / .abi file is used only to produce the trace and base calls, and is never logged or stored. The same parsing is available via the REST API and the MCP server.
What do the channel colors mean?
The four dye channels use the classic ABI palette: G is black, A is green, C is blue and T is red. The channel order is read from the file's FWO_ tag, so channels are always mapped to the correct base.
Can I export the read or the figure?
Yes. Copy or download the base calls as a FASTA record, and export the electropherogram as a vector SVG or a high-resolution PNG for your notebook or a figure.
How do I judge read quality?
The viewer shows the read length and mean Phred quality. Clean single peaks and high quality indicate a reliable read; low, broad or overlapping peaks and low-quality stretches (usually near the ends) are the regions to trim before downstream analysis.
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