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Hi,any one have experience of denovo asembly of solexa reads having 1x coverege by using velvet.
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It is not possible to assemble 1x coverage data, because no read will overlap any other read.Originally posted by bioenvisage View Post -
and to add to Torst, most de novo assemblers will have significant problems until you sequence to between 10X and 20X coverage at a minimum.Comment
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Some reads will be overlapping.
About one third locations have 0x coverage, one third 1x, fewer 2x, even fewer 3x ...Comment
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This is simply not enough coverage. You might be able to detect some SNPs, and assembled a few short regions, but that's it. Sorry.Originally posted by 0Gen View PostComment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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