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Old 02-19-2009, 03:19 AM   #1
mingkunli
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Default gap alignment and local alignment?

which software is capable of doing gapped alignment besides SOAP?
which software is capable of doing local alignment that can align different part of read to different ref region?
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Old 02-19-2009, 04:37 AM   #2
lh3
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novoalign and bwa find gaps on single-end reads; maq finds gaps on paired-end reads only. New cross_match is recommended to do local alignment. You may also try ssaha2, shrimp and BFAST(?). If I am right, they all do gapped alignment.
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Old 02-19-2009, 05:45 AM   #3
mingkunli
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thanks, lh3.
Among them, which can take use of quality score? I know your MAQ can, SOAP seems can't(although it can display the quality score).
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Old 02-19-2009, 12:13 PM   #4
andpet
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Mosaik from the Marth Lab also does gapped alignment and uses quality values. It also provides functions like alignment merging, sorting, visualization and is well documented.

Andreas
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