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Does anyone know any software that will close gaps between contigs using Solexa mate-pair data (insertion ~2500kb)?
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Are you saying u can generate reads with an insert size of 2500kb? -
Woops! 2500b
)
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We do...
At the Sanger Insitute, we developed some software which is not published yet for filling the gaps using solexa reads. Is working really well, and it let you close around 60% of the gaps (in average). We haven't test it using that length of insert size but the projections tell us that it would close more gaps with larger insert sizes.
Also we have things for error correction that uses solexa reads too.
Contact me if you want more details.Comment
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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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