I am having a hard time understanding the bwtsw option in bwa index command.
1. What does this do that is different from the is option and why is it recommended for longer (>10 MB) reference genomes ?
2. Does it have anything to do with the actual alignment with indels (using Smith-Waterman) ? Or is the "sw" in "bwtsw" just a coincidence ?
3. What is the relation between this and bwasw ? Should I use both or neither ? Or are they completely independent of each other ?
4. Does using this option change the alignment output or is it just a better/faster indexing technique for large reference genomes ?
Sowmya
1. What does this do that is different from the is option and why is it recommended for longer (>10 MB) reference genomes ?
2. Does it have anything to do with the actual alignment with indels (using Smith-Waterman) ? Or is the "sw" in "bwtsw" just a coincidence ?
3. What is the relation between this and bwasw ? Should I use both or neither ? Or are they completely independent of each other ?
4. Does using this option change the alignment output or is it just a better/faster indexing technique for large reference genomes ?
Sowmya
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