Base calling software tools | Sanger sequencing data analysis
Base calling is the process by which raw data from the sequencing instrument is converted to nucleotide sequences. This is performed by base calling software that is usually run from the instrument itself. As we have seen, sequencing instruments generate raw data in different forms (fluorescence intensity, electrical impulse, etc.), and therefore base calling is specific to the particular platform being used.
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.
A package to estimate a probability of error for each base-call. Phred identifies a base sequence from a fluorescence "trace" data generated by an automated DNA sequencer using electrophoresis and 4-fluorescent dye method. Phred produces significantly fewer errors in the data sets examined than other methods, averaging 40–50% fewer errors. It’s used into the Human Genome Project.
Allows users to manipulate trace files derived from DNA sequencing instruments to perform quality and base calling, including mixed one. TraceTuner is an open source program which can be used within sequencing projects involving drosophila melanogaster and human genome. The software has been developed with the aim of being easily incorporated into other applications such as forensic software.
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.
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.