How is mate alignment which may generate soft-clipping signature implemented in bwa?

Would one please describe the mate alignment algorithm that has been implemented in bwa? Is it kind of modified SW algorithm?

Thank you!

alignment

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updated 11.8 years ago by Biostar

• written 11.9 years ago by zhangz.cs •

Have you read the papers (the bwa mem paper is here)?

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written 11.9 years ago by Devon Ryan

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