Table 1.

Software for primary quality control of NGS data

Method name	Year published	PMID	Data type	Platform	Statistical method	Input requirements
BIGpre	2011	22289480	Illumina, 454	Perl	Correlation between forward and reverse reads, trimming low-quality reads	FASTQ
FastQC	2010	–	any	Java	Sequence length, quality, k-mers presence reports	FASTQ, SAM/BAM
HTQC	2013	23363224	Illumina	C++	Tail trimming, filter by quality/length/tile	FASTQ
QC-Chain	2013	23565205	any	C++	Quality assessment, trimming, filtering unknown contamination	FASTQ
Qualimap	2012	22914218	any	Java, R	Alignment biases detection, sample comparison	SAM/BAM
PRINSEQ	2011	21278185	any	Perl	Sequence complexity, duplicates, occurrence of Ns and poly-A/T tails, tag sequences reports	FASTQ, FASTA
PIQA	2009	19602525	Illumina	R	Assess the clusters density per tile, base-calls proportions per tile/cycle	FASTQ
FastUniq	2012	23284954	any	C++	De novo PCR duplicates removal for paired short reads	FASTQ