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  • lgoerlitz
    Junior Member
    • May 2009
    • 2

    Which assembly algorithms to benchmark?

    Hi everyone,

    We're relatively soon going to do some in-house benchmarking of our own algorithms which will be published in a white paper. We're thinking separate benchmarks for short and long reads for both for de novo and reference assembly, would be the ideal way to test.

    Although we have some ideas of what algorithms to benchmark against, it would be great to hear what you guys would like to see benchmarked and why!? We can't promise to include all suggestions, but we'll do our best! Also if you have other input relating to a benchmark setup, you're most welcome to share your thoughts

    Cheers,
    Lasse, CLC bio

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  • GATTACAT
    Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing
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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.
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  • SEQadmin2
    Nine Things a Sample Prep Scientist Thinks About Before Sequencing
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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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