Chromatogram processing software tools | Sanger sequencing data analysis
Modern applications of Sanger DNA sequencing often require converting a large number of chromatogram trace files into high-quality DNA sequences for downstream analyses. Relatively few software tools are available to assist with this process.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Assists molecular biologists without much expertise in bioinformatics in managing, analyzing and visualizing their data. unipro UGENE supports multiple biological data formats and allows the retrieval of data from remote data sources. It integrates widely used bioinformatics tools within a common user interface. The tool includes a visual environment for creating reusable workflows that can be launched on local resources or in a high-performance computing (HPC) environment.
Conducts next generation sequencing (NGS) investigation. Geneious provides visual sequence alignment and editing, sequence assembly, comprehensive molecular cloning and phylogenetic analysis. It increases process efficiency and improves data organization. This tool enables the importation and conversion of a vast range of data types and offers a solution to customize researchers’ algorithms.
Analyses the Sanger sequencing data and provides an easy-to-use one-step solution for genetic testing data analysis. ODS seamlessly integrates base calling, single nucleotide variation (SNV) identification, and SNV annotation into one single platform. It also allows laboratorians to manually inspect the quality of the identified SNVs in the final report. ODS can significantly reduce the data analysis time therefore allows Sanger sequencing-based genetic testing to be finished in a timely manner.
Assists for DNA chromatograms analysis of Sanger sequenced DNA barcode. PIPEBAR automatizes the processing of large number of trace files. This software can generate quality reports and allows visualization of quality values of the barcode sequence bases, by specifying a threshold of the minimum accepted PHRED value. It proceeds by considering all frames of translation and selecting the frames that contain the largest open reading frame (ORF).
Contains several tools for analyzing Sanger Sequencing data files in R, including reading .scf and .ab1 files, making basecalls and plotting chromatograms. sangerseqR offers functions to generate a chromatogram from a sangerseq class object, to run the Poly Peak Parser shiny app in the systems default browser, to allow the user to retrieve results from and assign values to sangerseq-class objects and many others.
Simplifies the generation of high-quality finished sequences from a large number of trace files. SeqTrace is designed for sequencing projects that require converting trace files directly into high-quality, finished sequences. It can be used as a general-purpose trace viewer and editor. This tool allows users to save projects to an external file using a custom file format that conserves the state of the project and all of its sequences.
Systematically identify and correct sequencing errors in multiple sequence alignments (MSAs) that relies on chromatogram data. CG constructs a report for every ambiguous character/site that allows the user to inspect the corresponding chromatogram positions. It integrates a chromatogram editing via automatically generated reports. This tool procceds by scaning an initial MSA for potential sequencing errors.
Allows to view and edit chromatograms (traces) from automated Sanger sequencers. Chromas contains format conversion options and batch processing functions to handle many files at once. The software provides several features, such as automatic removal of low-quality sequence or vector sequences when quality data is available, reversing and complementing the sequence and chromatogram, searching for subsequences by exact matching or optimal alignment and displaying translations in 3 frames along with the sequence.
Provides Sanger data sequence assembly and analysis. SeqMan Pro is an application that provides next-generation visualizations and analysis of projects. It helps to discover variants, analyzes coverage, and annotates users’ consensus. These projects can then be exported to GenVision for graphical data of the publishing quality assembly. It can also be used for Single-Nucleotide Polymorphism (SNP) calling and quality-based sequence end trimming. This application is a part of Lasergene Molecular Biology Suite.
Allows DNA, RNA, and protein sequence data analysis. CLC Main Workbench is a comprehensive workbench. A primer design functionality offers graphical interaction during the primer selection process. The software also allows to show the annotations of the individual sequences in a multiple sequence alignment, offers graphically advanced in silico cloning and design of vectors, BLAST searches on protein and DNA sequences, and other feature such as Assembly, Phylogeny, Workflow, Molecular structure visualization and development of plug-ins.
A DNA sequencing analysis software capable of performing variant analysis of up to 2000 Sanger sequencing files generated by Applied Biosystems Genetic Analyzers, MegaBACE as well as Beckman CEQ electrophoresis systems.
Handles DNA sequencing traces. TraceViewer is a standalone software dedicated to the visualization and the management of traces, that can be processed in conjunction with the Phred software. This program is able to support multiple formats and proposes several options for editing data of interest including settings of color background and representation of results as bars or numbers with various color schemes.
Assists users with DNA sequence analysis. Sequencher is a graphical application that integrates the Cufflinks suite for in-depth transcript analysis and differential gene expression of RNA-Seq data. It can generate unique data visualizations using customized plots and graphs that produces ready-to-print graphs. This model also includes an extensive Sanger analysis features.
Allows sequence assembly and tracing of data and Illumina and Roche 454 flowgrams into contigs. DNA Dragon is a contig assembler that supports several formats, including FASTA, GenBank or EMBL, as well as several trace file and next-generation sequencing (NGS) file formats.