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Maq Still Leading the Way

Dan Koboldt of the MassGenomics blog will be presenting a poster at this year's Marco Island sequencing meeting evaluating short read aligners. He's compiled a partial list of aligners, which include first and foremost, Maq. "It’s safe to say that we decided to gamble on Maq over a year ago, and so far, the bet has paid off," he writes. Other options include Novoalign, Bowtie, cross_match, RMAP (which he hears the developers have stopped working on), and SOAP ("probably a tool to watch"). While his evaluations seem to beg for aligners that can handle gaps and paired end reads, his main criteria are speed, compatibility with in-house platforms, and "aligners that can beat Maq -- in performance, features, or sensitivity -- and that's not easy to do. Maq is fast and does quality-based alignment, single or paired-end, assembly, SNP calling… there's a reason why the rest of the industry seems to be conforming to it," he writes.

The Scan

Tens of Millions Saved

The Associated Press writes that vaccines against COVID-19 saved an estimated 20 million lives in their first year.

Supersized Bacterium

NPR reports that researchers have found and characterized a bacterium that is visible to the naked eye.

Also Subvariants

Moderna says its bivalent SARS-CoV-2 vaccine leads to a strong immune response against Omicron subvariants, the Wall Street Journal reports.

Science Papers Present Gene-Edited Mouse Models of Liver Cancer, Hürthle Cell Carcinoma Analysis

In Science this week: a collection of mouse models of primary liver cancer, and more.