|NextSeq 550 System||1 sample per run (based on eukaryotic genome finishing)||Up to 2 x 150 bp|
|HiSeq 2500 System||10 to 15 samples per run (dual flow cell; based on eukaryotic genome finishing)||Up to 2 x 150 bp|
Using a combination of short and long insert sizes with paired-end sequencing results in maximal coverage of the genome for de novo assembly. Because larger inserts can pair reads across greater distances, they provide a better ability to read through highly repetitive sequences and regions where large structural rearrangements have occured. Shorter inserts sequenced at higher depths can fill in gaps missed by larger inserts sequenced at lower depths. Thus a diverse library of short and long inserts results in better de novo assembly, leading to fewer gaps, larger contigs, and greater accuracy of the final consensus sequence.