Someone asked me whether it makes sense to remove duplicate reads to get the library size down to fit RAM limit. I think it is a bad strategy as explained here -
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That's a good point. Some filtering is necessary to take care of pileup of reads due to biases. I do that for alignment and SNP discovery, but think twice about it during de novo assembly. If no underlying genome is known, it is hard to tell whether the duplicated reads come from error or real sequence.
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It does not work that way for K-mer based assembler. Would you please explain your rationale? Why would one get false contigs?
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