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I want to know how hgap select the seed. The paper says it selects the seed with more than 20x coverage, but doesn't say how it counts the coverage.
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The seed will be selected automatically if you input the expected genome size. Coverage is a simply number of bases / genome size. -
Do that mean the automatically selected seeds are long enough and has enough coverage? Does it calculate kmer frequency?Comment
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HGAP is an overlap consensus based assembler and thus no kmer statistics are computed during the assembly process.Originally posted by Rui Guo View Post
As rhall stated, When you set up the run, you input a Genome Size (bp). The algorithm will sort the subreads by length, compute the quantity of bases necessary to obtain appropriate coverage for the Genome Size (bp) that you input during setup and select the longest data necessary to obtain the 30X coverage.
See this for more details:
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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.
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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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