Simple and Scalable Genome Analysis with Transposase Enzyme Linked Long-Read Sequencing (TELL-Seq): From Haplotype Phasing to De Novo Assembly in a Tube

摘要

Haplotype phasing of genomes and de novo assembly of novel genomes are major hurdles for short read based next generation sequencing platforms. Long sequence reads are essential to overcome the significant sequence homology on some regions of the genome. Several NGS library technology breakthroughs recently have demonstrated barcode linked-read sequencing method can effectively generate long read like information and successfully applied for human genome phasing, structural variation detection or de novo assembly of other genomes. However, they either require expensive capital expenditure on a special instrument or are not scalable for commercial adoption yet due to sophisticated barcode generation. We have developed a simple and scalable NGS library technology, Transposase Enzyme Linked Long-read Sequencing (TELL-SeqTM), to use short NGS reads for genome scale haplotype phasing and/or de novo genome assembly. Several million uniquely barcoded beads are used to generate linked reads, which could be linked as long as a hundred kilobases, by strand transfer reactions using transposase in a PCR tube with a standard NGS laboratory setting. TELL-Seq library procedure takes approximately 3 hours and multiple samples can be easily processed parallelly in a 96-well format when needed. The library protocol can be adjusted and used for various sizes of genomes from bacteria to human. Using TELL-Seq we are able to generate comparable and excellent haplotype phasing results on a NA12878 human sample, and successfully de novo assembly on an E. coli and an Arabidopsis thaliana. More applications and analysis solutions are being developed for TELL-Seq library technology. Articles from Journal of Biomolecular Techniques : JBT are provided here courtesy of The Association of Biomolecular Resource Facilities.