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Similar Threads
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| Thread | Thread Starter | Forum | Replies | Last Post |
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02-15-2012, 04:12 AM
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#1 |
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Member
Location: seoul Korea Join Date: Mar 2011
Posts: 19
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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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02-15-2012, 04:19 AM
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#2 |
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Member
Location: Germany Join Date: Jun 2011
Posts: 54
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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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02-15-2012, 05:18 AM
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#3 |
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Senior Member
Location: Graz, Austria Join Date: Feb 2010
Posts: 219
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a very popular algorithm for 454 reads is SSAHA2
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02-15-2012, 06:24 AM
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#4 |
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Senior Member
Location: amsterdam Join Date: Jun 2009
Posts: 133
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a newer version of SSAHA2 is SMALT.
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02-15-2012, 06:31 AM
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#5 |
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Super Moderator
Location: US Join Date: Nov 2009
Posts: 437
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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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