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Old 04-10-2009, 07:27 AM   #1
AnamikaDarwin
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Question BWA Read Length

Hello,

What is the maximum read length that can be used in BWA?

Thanks,
Anamika
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Old 04-11-2009, 12:47 AM   #2
lh3
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In principle, it works with kb long reads, but do not try that. First it will be very slow under the default configuration and second, it requires the full reads to be aligned which is not ideal for long reads as long reads are more likely to be interrupted by SV and misassembly. I have tried ~200bp reads. It works well, but not nicely.
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