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Old 01-22-2009, 08:13 AM   #1
Salmon
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Default Homopolymer error in 454 sequencing data

Hello,
I am currently working on genome assembly. our reads data is from 454 sequencing. First we assembled contigs using Newbler. However, when we compared our built genome with a reference genome (very close relationship), we found several genes were separated into two or three pieces because of the frame shift. After checked the reads data and reference data, we think it may cause by homopolymer errors because homopolymer error is very common in 454 sequencing data.
In order to solve the homopolymer problem, should I re-assemble reads data using other assembler such as MIRA? Or does anyone give us some suggestions on homopolymer error?
Thanks.
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Old 01-23-2009, 05:40 AM   #2
rs705
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A commercial assembly tool that may help is one from DNASTAR called SeqMan NGen. It avoids some of the issues related to homopolymeric errors seen in other assemblers. If you contact the company you can also get their technical support people to help determine if the issue is related to this or some other issue as you are evaluating the software.
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Old 01-29-2009, 05:53 AM   #3
mingkunli
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I have compared their results, Seqman can solve the problem to a certain degree, although it causes other problem in my data.
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Old 02-06-2009, 09:08 AM   #4
shaohua.fan
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hi, i don't think MIRA will do a better job, since the contigs(454 raw reads) i am analysing were assembled by MIRA, i also find some contigs are extremely similar, the differences are always found in the homopolymer region.
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