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.
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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