2 MATERIALS AND METHODS
easyfm can be used both by sophisticated data scientists and non-technical users who need an intuitive interface. The original intent for producing easyfm was to reduce reliance on any command lines/scripts or web-based platforms, by creating a standalone lightweight program with substantially reduced computational demands.easyfm provides key benefits in convenience, accessibility, and reproducibility because it does not include any heavyweight NGS data assembly, mapping and clustering workflows. easyfm can execute any pre-assembled genome/transcriptome FASTA files by selecting CPU numbers on a user’s desktop. While it mainly focuses on point-and-click analysis for less technical users, Log and Help functions could provide an interactive experience for monitoring and iterating on an executed code.
The easyfm work modules can provide support for post-processing, filtering, format conversion, and generating results to your given data (e.g. FASTA/Q files). It integrates four Python libraries and two executable programs with additional visualisation and conversation tools (mostly many well-established open-source Python packages) (Table 1). BLAST and indexing features provide the foundation for easyfmwith approaches for all four work modules (BLAST, BLAT, ORF, and File Manipulation). While the user is required to select a module to execute, the user has full control over which input (including compressed files: *.gz) and output files/folders can be selected. easyfm also generates several output files (mostly in a tab-separated text file) that can be opened with standard text editors or Excel. To support work modules, easyfm also has a secondary window— Project Folder, Help and Log— that integrates with work modules (Figure 1). In addition, further assistance and information can be obtained via Help and Log to improve processes and performance. easyfm also contains all necessary dependencies. Simply unzip the folder and double-click easyfm.exe after downloading the program. Documentation, along with tutorials, is available at https://github.com/TaekAndBrendan/easyfm, and links to theeasyfm download (https://github.com/TaekAndBrendan/easyfm/raw/main/windows/easyfm.7z).
TABLE 1. Software packages integrated into easyfm and their applications