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Examining the Sequencing Sample Prep 'Ecosystem'

While Daniel MacArthur at Genetic Future is blogging about Nick Loman's attempt to "estimate the number of second-generation sequencing machines in the wild," Keith Robison at Omics! Omics! is surveying the second-gen sample prep "ecosystem." He writes that because each manufacturer supplies its own collection of sample preparation kits, things have become complicated for third party suppliers that produce sample prep options. "For example, targeted re-sequencing using hybridization really needs to have the sequencing adapters blocked with competing oligos — and those will depend on which platform the sample has been prepared for," Robison writes, adding that "it would [be] great for benchmarking instruments if precisely the same library could be fed into multiple machines — and it would be great for researchers looking to buy sequencing capacity on the open market to be able to defer committing to a platform to the last minute." Of course, he says, it's not that simple, because selling kits is a "potentially lucrative" business teeming with "nasty (and silly) legal strategies."

The Scan

Gone, But Now Reconstructed SARS-CoV-2 Genomes

In a preprint, a researcher describes his recovery of viral sequences that had been removed from a common database.

Rare Heart Inflammation Warning

The Food and Drug Administration is adding a warning about links between a rare inflammatory heart condition and two SARS-CoV-2 vaccines, Reuters reports.

Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.