NanoBLASTer: Fast alignment and characterization of Oxford Nanopore single molecule sequencing reads

Abstract

The quality of the Oxford Nanopores long DNA sequence reads has been, to date, lower than other technologies, causing great interest to develop new algorithms that can make use of the data. So far, alignment methods including LAST, BLAST, BWA-MEM and GraphMap have been used to analyze these sequences. However, each of these tools has significant challenges to use with these data: LAST and BLAST require considerable processing time for high sensitivity, BWA-MEM has the smallest average alignment length, and GraphMap aligns many random strings with moderate accuracy. To address these challenges we developed a new read aligner called NanoBLASTer specifically designed for long nanopore reads. In experiments resequencing the well-studied S. cerevisiae (yeast) and Escherichia coli (E. coli) genomes, we show that our algorithm produces longer alignments with higher overall sensitivity than LAST, BLAST and BWA-MEM. We also show that the runtime of NanoBLASTer is faster than GraphMap, BLAST and BWA-MEM.