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Three Insights for Choosing the Best DNA Size Selection Method for Your Project

With so many methods for DNA size selection, it can be confusing to determine which is best for your project. Fortunately, academic researchers have evaluated many DNA size selection methods for a range of applications, and their conclusions provide some useful insight for the community. Double-Digest RAD-Seq Based on the original protocol for restriction site […]

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In Genomics & Epigenetics 14th of December, 2016
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How Does Automated Electrophoresis Perform DNA Size Selection?

Anytime lab processes get automated by a sophisticated scientific instrument, there can be a “black box” effect, leading users to wonder what’s going on in there. For DNA electrophoresis, it’s no different. It’s easy to see what’s happening in a manual gel, but the automated gel-based DNA size selection platforms can be more mysterious. Automated […]

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In Genomics & Epigenetics 15th of November, 2016
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DNA Sizing Tutorial: When to Use Manual Gels, Beads, and More

There are several methods for size-selecting DNA fragments prior to sequencing. How do you choose which is best? Here’s a look at various options, plus considerations to help you determine when to use each one. Manual Gels Virtually every student in a biology lab knows how to prepare and cut a manual gel—but their ubiquity […]

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In Genomics & Epigenetics 1st of September, 2016
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For Better NGS Assemblies, Use More Precise DNA Size Selection

It may not be intuitive that a sample preparation step like DNA size selection would have a significant impact on downstream data analysis, but NGS users have proven that it does. Indeed, the precision of your size selection (or lack thereof) can make or break a genome assembly. Consider the alignment challenge for paired-end reads: […]

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In Genomics & Epigenetics 28th of July, 2016
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The Art of Size Selection for Small RNAs

Size selection is a critical step in NGS pipelines, but may be most challenging for studies of small RNAs. The concept behind size selection is simple: separate a sheared DNA or cDNA sample by fragment size, and then use the resulting sizes to remove unwanted fragments. This is a tried-and-true way to get rid of […]

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In Genomics & Epigenetics 17th of March, 2016
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Whole-Sample Fractionation for NGS Pipelines with the SageELF

In many NGS workflows, you want more than just a single slice of your DNA sample — but most size selection methods make it difficult to salvage multiple bands or size ranges of DNA. This is especially important when dealing with precious samples or with certain applications where it’s useful to have libraries with multiple […]

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In Genomics & Epigenetics 17th of March, 2016
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Size Selection read on

For Long-Read Sequencers, Size Selection Is Key

It took scientists a little while to warm up to long-read sequencing, but now you couldn’t pry most of them away from their sequencers with a crowbar. Long reads — we’re talking 10,000 bases and more — provide a level of contiguity and completeness in genome assemblies that simply isn’t possible with short-read sequencers. They […]

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In Genomics & Epigenetics 9th of February, 2016
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High-Throughput DNA Size Selection with the PippinHT

DNA size selection is a necessary but thankless task. Manual DNA sizing conjures images of postdocs slaving for hours over gels, trying to cut out specific bands with improbable accuracy. Automated DNA sizing, while vastly improving the precision and reproducibility of size selection, has historically been too low-throughput for many NGS labs or too imprecise […]

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In Genomics & Epigenetics 9th of February, 2016
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Why DNA Size Selection Matters in NGS Pipelines

Of all the sample prep steps necessary for next generation sequencing, DNA size selection may have the greatest impact on quality of results. After all, ineffective sizing can waste sequencing capacity on low molecular weight material such as adapter-dimers or primer-dimers, while imprecise sizing can prevent bioinformaticians from producing accurate assemblies. High-quality size selection can […]

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In Genomics & Epigenetics 15th of January, 2016