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Old 02-15-2012, 04:12 AM   #1
Location: seoul Korea

Join Date: Mar 2011
Posts: 19
Default need mapping solutions for 454 reads

I tried to map 454 reads with GS reference mapper.
I want to map them with different algorithm.
Could you recommed any software good for 454 reads?
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Old 02-15-2012, 04:19 AM   #2
Location: Germany

Join Date: Jun 2011
Posts: 54

You could try GMAP or bwa (with sw option set). Do you have PE or SE reads and do you have cDNA or genomic reads?
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Old 02-15-2012, 05:18 AM   #3
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Location: Graz, Austria

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Posts: 219

a very popular algorithm for 454 reads is SSAHA2
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Old 02-15-2012, 06:24 AM   #4
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Location: amsterdam

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a newer version of SSAHA2 is SMALT.
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Old 02-15-2012, 06:31 AM   #5
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Location: US

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SMALT and BWA-SW are good. We have had some improved results by splitting the reads at homopolymers.
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