We have applied maq and bwa to align the same production data, and we see an obvious difference on the number of aligned reads between maq and bwa, especially a decrease in the number with longer read length.
This issue is critical, is it a drawback of bwa that aligns much less reads than maq? I am using the default options for bwa running, anyone has experience to increase the aligned reads dramatically by using different bwa options?
I don't know if it is a bottleneck of BWT algorithm even it is much faster than maq. If so, I might have to think again if I am really in favor of bwa. Now bwa is pushed forward, anyone has comments of this issue?
thanks
This issue is critical, is it a drawback of bwa that aligns much less reads than maq? I am using the default options for bwa running, anyone has experience to increase the aligned reads dramatically by using different bwa options?
I don't know if it is a bottleneck of BWT algorithm even it is much faster than maq. If so, I might have to think again if I am really in favor of bwa. Now bwa is pushed forward, anyone has comments of this issue?
thanks
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