gap alignment and local alignment?

mingkunli · 02-19-2009, 03:19 AM

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?

lh3 · 02-19-2009, 04:37 AM

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.

mingkunli · 02-19-2009, 05:45 AM

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).

andpet · 02-19-2009, 12:13 PM

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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02-19-2009, 03:19 AM	#1
mingkunli Member Location: Germany Join Date: Jan 2009 Posts: 41	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?

02-19-2009, 04:37 AM	#2
lh3 Senior Member Location: Boston Join Date: Feb 2008 Posts: 693	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.

02-19-2009, 05:45 AM	#3
mingkunli Member Location: Germany Join Date: Jan 2009 Posts: 41	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).

02-19-2009, 12:13 PM	#4
andpet Member Location: Germany Join Date: Jul 2008 Posts: 26	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