PhageGT: dsDNA phage genome termini analysis software

Abstract:

[Background] With the reduction of sequencing costs, more and more scientists have used high-throughput sequencing (HTS) technology to study the genome sequence of phages. Some termini analysis theory or methods were developed by some scientists to determine genomic terminal sequences of dsDNA phages. However, these methods are based on the commands under the Linux system. There is no software under the Windows operating system. [Objective] A free software PhageGT, which can be used in the Windows platform, was developed and can detect details of the genome termini of dsDNA phages genome using HTS Reads data and the complete sequence of phage genome. [Methods] A dialog-based Microsoft foundation classes (MFC) application was developed by Visual Studio 2019 and C++ language. Corresponding algorithms were designed for reading HTS Reads data and calculation. [Results] The frequency of the Reads can be calculated and ranked in descending order. The ratio of the highest frequency of the extracted sequence to the average frequency of the sequence (R) can be calculated. [Conclusion] This software PhageGT is very practical. The software PhageGT and all the test data used in this article can be downloaded for free from the website, https://zenodo.org/record/4543997#.YEhtG50zYhQ.