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Fun with Unix and Sequencing Data

There's an on-going thread at SEQanswers ("Hello - I use to think I was good with a computer") with tips on dealing with sequencing data. First, Jon_Keats posts some gems that he recently learned, namely that "my boss should have made me read and do the 'Unix and Perl for Biologist' tutorial years ago" and "BWA can align on my laptop ... cool ... next-gen/2nd gen alignment on a laptop and I [thought] I needed a super computer." Keats later posts a more technical fast-start guide for using Unix and Xcode as well as compiling applications.

HT: Nils Homer

The Scan

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.

Researchers Retrace Key Mutations in Reassorted H1N1 Swine Flu Virus With Avian-Like Features

Mutations in the acidic polymerase-coding gene boost the pathogenicity and transmissibility of Eurasian avian-like H1N1 swine influenza viruses, a PNAS paper finds.

Genome Sequences Reveal Evolutionary History of South America's Canids

An analysis in PNAS of South American canid species' genomes offers a look at their evolutionary history, as well as their relationships and adaptations.

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.