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A Look at GATK

Dan Koboldt at MassGenomics says next-gen sequencing has presented some problems for the bioinformatics community in terms of the sheer amount of data being generated. Tools for sequencing data analysis are under demand for efficiency, flexibility, and scalability, he says. A key development in this field was the Sequence Alignment Map, but now, researchers at the Broad Institute have come out with the latest advance — the Genome Analysis Toolkit. "Essentially, GATK is a foundation of code that takes advantage of the SAM/BAM input format to simplify many of the common requirements for data analysis tools," Koboldt says. It can accommodate reads from any sequencing platform, support most sequence aligners, and recognize public database formats, he adds. "It strikes me that frameworks such as this, coupled with the latest 4-core, 8-core, even 50-core CPUs, may finally be bioinformatics' answer to the challenge of massively parallel sequencing," Koboldt says.

The Scan

Two J&J Doses

Johnson & Johnson says two doses of its SARS-CoV-2 vaccine provides increased protection against symptomatic COVID-19, CNN reports.

Pfizer-BioNTech Vaccine Response in Kids

The Pfizer-BioNTech SARS-CoV-2 vaccine in a lower-dose format appears to generate an immune response among children, according to the Washington Post.

Chicken Changes to Prevent Disease

The Guardian writes that researchers are looking at gene editing chickens to help prevent future pandemics.

PNAS Papers on Siberian Dog Ancestry, Insect Reproduction, Hippocampal Neurogenesis

In PNAS this week: ancestry and admixture among Siberian dogs, hormone role in fruit fly reproduction, and more.