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