Sequencing By Ligation Variation with Endonuclease V and Deoxyinosine and SAWTooth – The Sequencing Analysis Workbench Tool

Abstract

Sequencing-by-ligation (SBL) is one of several next-generation sequencing methods that has been developed for massive sequencing of DNA immobilized on arrayed beads (or other clonal amplicons). SBL has the advantage of being easy to implement and accessible to all because it can be performed with off-the-shelf reagents. However, SBL has the limitation of very short read lengths. To overcome the read length limitation, research groups have developed complex library preparation processes, which can be time-consuming, difficult, and result in low complexity libraries. Herein we describe a variation on traditional SBL protocols that extends the number of sequential bases that can be sequenced by using Endonuclease V to nick a query primer, thus leaving a ligatable end extended into the unknown sequence for further SBL cycles.
Additionally, virtually all next-generation sequencing platforms generate giga-base-pairs of data per run, often in the form of mate-paired short–reads. We anticipate the daily need to sequence, and subsequently align (map) to a reference genome, several billion mate-pair reads, or single sequence reads, in whole-genome sequencing of human samples. These reads may need to be aligned to a large reference genome, itself comprising several giga-base-pairs. An efficient algorithm to perform this mapping is essential given these large dataset sizes. Here we present the SawTooth suite of software applications whose core functionality is the efficient mapping of short-read sequencing data to a reference genome. SawTooth also implements several ancillary applications for validation and statistical analysis of mapping results.