Table 2. Next-generation sequencing and bioinformatics details obtained from FastQC software (Andrews, 2010) and QDD pipeline (Meglécz et al., 2010) for Lutjanus johnii, Protonibea diacanthus and Lethrinus laticaudis.

	Lutjanus johnii	Protonibea diacanthus	Lethrinus laticaudis
Genomic DNA extraction	Qiagen DNeasy	Qiagen DNeasy	Salting out
NGS Technology	IonTorrent | Ion318Chip	IonTorrent | Ion318Chip	Illumina® MiSeq
Library preparation	Iron ExpressTM	Iron ExpressTM
Type of reads	Single reads	Single reads	Paired-end reads
Number of reads	1,374,891	1,587,789	2,800,640
Merged reads	–	–	1,169,198
Reads length	8–620	8–618	300
Merged reads length	–	–	300–575
FASTQC
% GC	41	42	39
Sequence quality < Phred 20	yes at positions >325 bp	yes at positions >350 bp	no
Per sequence quality—Phred score	29	29	36
Sequence length distribution	peak at 350 bp	peak at 350 bp	plateau at 520–540 bp
QDD2
QDD2 pipe 1—Sequence preparation and microsatellite detection
Number sequence length ≥80 bp	1,235,685	1,405,082	1,169,198
Number sequence with microsatellite	109,641 (8.9%)	167,702 (11.9%)	130,269 (11.1%)
QDD2 pipe 2—Sequence similarity detection
Total # input sequences	109,641	167,702	130,269
Numer of unique consensus sequences	18,978	N/A	N/A
Number of singleton sequences	49,122	N/A	N/A
Number of reads in output	68,100	63,789	69,714
QDD2 pipe 3—Primer design
Total number of input sequences	68,100	63,789	69,714
Total number of sequences with target MS	67,461	63,785	69,714
Total number of sequences with primers	29,485	20,233	19,867
Filtering QDD output
Total # input sequences	29,485	20,233	19,867
Total # sequences after filtering criteria	121	97	103