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. 2023 Jul 12;3(1):vbad083.
doi: 10.1093/bioadv/vbad083. eCollection 2023.

TraceTrack, an open-source software for batch processing, alignment and visualization of sanger sequencing chromatograms

Kveta Brazdilova  1   2 , David Prihoda  1   2 , Quynh Ton  3 , Heath Klock  3 , Danny A Bitton  1
Affiliations

TraceTrack, an open-source software for batch processing, alignment and visualization of sanger sequencing chromatograms

Kveta Brazdilova et al. Bioinform Adv. .

Abstract

Motivation: Despite the advent of next-generation sequencing technology and its widespread applications, Sanger sequencing remains instrumental for molecular biology subcloning work in biological and medical research and indispensable for drug discovery campaigns. Although Sanger sequencing technology has been long established, existing software for processing and visualization of trace file chromatograms is limited in terms of functionality, scalability and availability for commercial use.

Results: To fill this gap, we developed TraceTrack, an open-source web application tool for batch alignment, analysis and visualization of Sanger trace files. TraceTrack offers high-throughput matching of trace files to reference sequences, rapid identification of mutations and an intuitive chromatogram analysis. Comparative analysis between TraceTrack and existing software tools highlights the advantages of TraceTrack with regards to batch processing, visualization and export functionalities.

Availability and implementation: TraceTrack is available at https://github.com/MSDLLCpapers/TraceTrack and as a web application at https://tracetrack.dichlab.org. TraceTrack is a web application for batch processing and visualization of Sanger trace file chromatograms that meets the increasing demand of industrial sequence validation workflows in pharmaceutical settings.

Supplementary information: Supplementary data are available at Bioinformatics Advances online.

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Conflict of interest statement

All authors are/were employees of Merck Sharp & Dohme LLC, a subsidiary of Merck & Co., Inc., Rahway, NJ, USA and may hold stocks and/or stock options in Merck & Co., Inc., Rahway, NJ, USA.

Figures

Figure 1.
Figure 1.
TraceTrack enables high-throughput matching of Sanger chromatograms files and reference sequences. (Top) TraceTrack is routinely and extensively used to validate sequences in subcloning work. Sanger sequencing trace files (.ab1 file format) are matched with reference sequences (.csv, .xslx, .fa and .gb file formats) via systematic MSAs. (Bottom) For each resultant alignment, TraceTrack reports consensus sequence alongside percentage coverage, identity and the type of detected mutations as well as enables users to interrogate trace files via a dedicated trace viewer
Figure 2.
Figure 2.
TraceTrack input page. (A) Users can upload hundreds of Sanger trace files and reference sequences for matching. (B) Settings page with options for choosing references and read directions. The data analysed in these screenshots are sequencing reads from Urva javanica and Crossarchus obscurus obtained from the Barcode of Life Database (Sujeevan and Hebert, 2007)
Figure 3.
Figure 3.
TraceTrack results page. (A) Table of trace and reference sequence alignments. (B) Alignment detail with colour-coded coverage and mutations. (C) Trace viewer showing the reference sequence and traces aligned to it
See this image and copyright information in PMC

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