Table 2. Comparison of the main features of the Next Generation Sequencing data quality control tools.

	QC-Chain	PRINSEQ	NGS QC Toolkit	Fastx_Toolkit	FastQC
Availablility	Scripts	Scripts; Web-based	Scripts	Scripts; Web-based	Scripts
Language	C++	Perl	Perl	C++	Java
Input file	FastQ, FastA	FastQ, FastA	FastQ, FastA	FastQ, FastA	FastQ, SAM, BAM
Output file	Text; graph	Text; graph	Text, graph, HTML file	Text; graph	Graph, HTML file
Operating system	Linux	Linux, Windows, MacOS, BSD, Solaris	Linux; Windows	Linux, MacOS, BSD, Solaris	Linux; Windows; MacOS
Parallel computing	multi-thread and multi CPU based	No	multi-thread and multi CPU based	No	No
Read-quality assessment and trimming	Yes	Yes	Yes	Yes	Only read- quality assessment
Contamination screening	de novo identification	No	No	No	No