Abstract: The present invention enables the determination by NGS of the full nucleotide sequence of one or more polynucleotides of interest that are more than 800 bp in length after only one round of PCR amplification and subsequent fragmentation by adding at least one known oligonucleotide index to at least one end of each polynucleotide to produce elongated polynucleotides, wherein each known oligonucleotide index added to each polynucleotide is unique; fragmenting the elongated polynucleotides; sequencing the resulting fragments with paired forward and reverse reads using bridge amplification and next-generation sequencing; sorting the paired sequences based on the known oligonucleotide; and performing manual or in silico assembly of the sorted paired sequences, thereby providing the full coding sequence of each of the multitude of polynucleotides.