Poly Peak Parser (sangerseqR) Review

Developer: Jonathon T. Hill & Bradley Demarest (Bioconductor / University of Utah)

Supported platforms: Windows, macOS, and Linux (R / Bioconductor sangerseqR package + local Shiny web UI)

Access: https://bioconductor.org/packages/sangerseqR/ (GitHub mirror)

Features

View Quality scores

Reads ABIF base quality arrays when present and focuses on peak amplitude ratio thresholds (default 0.33) to distinguish true secondary peaks from background noise.

View raw data

Yes, programmatically in R: traceMatrix() exposes processed chromatogram signals, while read.abif() provides access to original ABIF tags alongside peakPosMatrix() and peakAmpMatrix().

Assembly

Single-amplicon heterozygous indel phasing and allele separation (setAllelePhase()) against a supplied wild-type reference sequence (multi-read contig assembly is available via downstream Bioconductor package sangeranalyseR).

Input file formats

.ab1 (ABIF) and .scf, plus plain text/FASTA reference sequence.

Output file formats

Deconvoluted primary and secondary allele sequences, R chromatogram plots, and PDF trace exports.

Trimming

Yes—fixed 5′ and 3′ base trimming (trim5, trim3; default 30 bp ends in the Shiny UI) with shaded trim visualisation in chromatogram().

Integrated Blast

No.

Open multiple windows

Supported via R script plotting, multiple PDF graphics devices, or Shiny browser tabs.

Edit bases

Programmatic base-call tuning via peak ratio cutoffs rather than point-and-click manual editing.

ABI limits (regions outside of clear range region are displayed in gray)

No (trimmed regions can be shaded red or hidden in R chromatogram plots via showtrim).

Other functions

• Separates double-peak frameshift traces from CRISPR/Cas9 or F1 heterozygous PCR products without cloning
• PolyPeakParser() launches the interactive Shiny web app locally inside R
• Core dependency for R tools such as sangeranalyseR and CrispRVariants

Cost

Free and open source (GPL-2).

Comments

Note that the legacy University of Utah hosted Poly Peak Parser web server (yosttools.genetics.utah.edu) was retired in mid-2025, so active users should install the official Bioconductor sangerseqR package in R and launch the bundled PolyPeakParser() web interface locally. For a hosted zero-install alternative that performs similar indel deconvolution in your browser, try GEAR Genomics Indigo.

Return to the Trace Viewers overview or check trace quality online with QualTrace III Online.