TY - GEN
T1 - NanoBLASTer
T2 - 6th IEEE International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2016
AU - Amin, Mohammad Ruhul
AU - Skiena, Steven
AU - Schatz, Michael C.
N1 - Publisher Copyright:
© 2016 IEEE.
PY - 2016/12/30
Y1 - 2016/12/30
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85011024626&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85011024626&partnerID=8YFLogxK
U2 - 10.1109/ICCABS.2016.7802776
DO - 10.1109/ICCABS.2016.7802776
M3 - Conference contribution
AN - SCOPUS:85011024626
T3 - 2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2016
BT - 2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2016
PB - Institute of Electrical and Electronics Engineers Inc.
Y2 - 13 October 2016 through 15 October 2016
ER -