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Some Data to Play With

Both Keith Robison at Omics! Omics! and Dan Koboldt at Mass Genomics have been looking over data produced using Ion Torrent's 316 chip. Robison notes that the data set, a sequencing run of E. coli DH10B, contains 1.69 million reads, 1.53 million of which were 50 base pairs or longer. "No enormous gains in read length in this dataset, though the curve might be shifted towards longer," he writes, adding that the Broad Institute has been getting more than 2 million reads from its 316 chips. In addition, Koboldt calculated the average base quality of the first 1,600 reads. "You'll notice that, like early Illumina/Solexa data, average base quality declines along the length of the read," he says, noting that that these are variable-length reads. "Thus, it's possible that only the last few bases in each read are low-quality, which reduces the average score as you reach the end of the reads." He also found that substitutions were more likely to occur near the ends of the reads. "The 454-like homopolymer issue raises some concerns about using this platform for variant discovery," Koboldt adds. "Yet despite the errors, I'm impressed at how rapidly the technology has matured."

The Scan

Alzheimer's Risk Gene Among Women

CNN reports that researchers have found that variants in MGMT contribute to Alzheimer's disease risk among women but not men.

Still Hanging Around

The Guardian writes that persistent pockets of SARS-CoV-2 in the body could contribute to long COVID.

Through a Little Spit

Enteric viruses like norovirus may also be transmitted through saliva, not just the fecal-oral route, according to New Scientist.

Nature Papers Present Method to Detect Full Transcriptome, Viruses Infecting Asgard Archaea, More

In Nature this week: VASA-seq approach to detect full transcriptome, analysis of viruses infecting Asgard archaea, and more.