Hello forum members,
I'm running GS de novo Assembler on 454 junior data and I'm wondering if folks groom the data based on qual scores before running the assembler. I can pass in the sff file, which contains the qual data, so I assume the assembler does something with the qual data. The qual scores on isotigs from a recent run were very good and I have also read from others that using the sff file produced a better assembly than simply passing the read file without the quals. I tried to get an answer from the manual (as far as qual cutoff for reads), but found none.
Any ideas?
I'm running GS de novo Assembler on 454 junior data and I'm wondering if folks groom the data based on qual scores before running the assembler. I can pass in the sff file, which contains the qual data, so I assume the assembler does something with the qual data. The qual scores on isotigs from a recent run were very good and I have also read from others that using the sff file produced a better assembly than simply passing the read file without the quals. I tried to get an answer from the manual (as far as qual cutoff for reads), but found none.
Any ideas?
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