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Old 02-15-2012, 03:12 AM   #1
eoh001
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Location: seoul Korea

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Default need mapping solutions for 454 reads

Hello
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?
Thanks!!!!
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Old 02-15-2012, 03:19 AM   #2
lukas1848
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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, 04:18 AM   #3
ulz_peter
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a very popular algorithm for 454 reads is SSAHA2
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Old 02-15-2012, 05:24 AM   #4
KaiYe
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a newer version of SSAHA2 is SMALT.
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Old 02-15-2012, 05:31 AM   #5
adaptivegenome
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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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