easyfm: An easy software suite for file manipulation of Next Generation
Sequencing data on desktops
Abstract
Storing and manipulating Next Generation Sequencing (NGS) file formats
for understanding biological phenomena is an essential but difficult
task in the life sciences. Yet, most methods for analysing NGS data
require complex command-line tools in high-performance computing (HPC)
or web-based servers and have not yet been implemented in comprehensive,
easy-to-use software. Here we present easyfm (easy file manipulation), a
free standalone Graphical User Interface (GUI) software with Python
support that can be used to facilitate the rapid discovery of target
sequences (or user’s interest) in NGS datasets for novice users (more
accessible to biologists). It enables them to perform end-to-end
reproducible data analyses using a desktop application (Windows, Mac and
Linux). Unlike existing tools, the GUI-based easyfm is not dependent on
any HPC system and can be operated without an internet connection. For
user-friendliness and convenience, easyfm was developed with four work
modules and a secondary GUI window, covering different aspects of NGS
data analysis, including post-processing, filtering, format conversion,
generating results, real-time log, and help. In combination with the
executable tools (BLAST+ and BLAT) and Python, easyfm allows the user to
set analysis parameters, select/extract regions of interest, examine the
input and output results, and convert to a wide range of file formats.
To help augment the functionality of existing web-based and command-line
tools, easyfm, a self-contained program, comes with extensive
documentation (https://github.com/TaekAndBrendan/easyfm). This specific
benefit allows easyfm to seamlessly integrate visual and interactive
representations of NGS files, supporting a wider scope of bioinformatics
applications in the life sciences.