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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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I think duplicated reads removed to avoid biases that resulted from library preparation (for example) and not for reduction of data for de-novo assembly.
Ilia -
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.Comment
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So when you assemble reads in to contigs, you will prefer that at least several reads will support the assembly. If you will have identical reads, you might obtain false contigs.
IliaComment
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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?Comment
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Let me rephrase my last comment:
If duplicated reads don't contribute to downstream the de novo assembly pipe, it will be good idea to remove them.
IliaComment
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Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM
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