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6 weeks to apply for a PhD with me at the University of Bath, developing new machine learning and statistical methods for studying bacterial killability by phage. Tremendous data from edze westra, very exciting project! findaphd.com/phds/project/a…

This is was major move to unlock DeepTrio’s full potential. If you are still using DeepVariant for trios, consider switching to DeepTrio, it should be better at de novo detection.

Tens of thousands of Bangladeshi citizens joined students who have been protesting a quota system for government jobs that benefits certain groups, including the descendants of those who fought for independence from Pakistan. Here's what to know. nyti.ms/3Lv0uLG

Bangladesh has enforced a nationwide curfew to quash student-led protests against government job quotas, with the military and police patrolling the streets of the capital, Dhaka aje.io/libh1p

Our fast haplotagging paper is now published (nature.com/articles/s4146…) - see the earlier thread for a summary. Thanks to Kishwar Alexey Kolesnikov for leading the work and collaborators: @Johngorzynski, Sneha D. Goenka, euan ashley, Miten Jain, Karen Miga, @BenedictPaten

Release of DeepSomatic v1.7 (github.com/google/deepsom…). Now supports tumor-only applications, now supports FFPE-prepared samples with specific models. New models to support exome and ONT. Improved accuracy and runtime improvements.

Transformer-based polishing approach DeepPolisher's manuscript is now live. Mira Mastoras polished 180 assemblies using DeepPolisher for the next human pangenome release. Collaboration with @BenedictPaten Mobin Asri. PM Andrew Carroll and eng mng Pi-Chuan Chang. biorxiv.org/content/10.110…

Initiated in 2023 by Maria Nattestad and Been Kim, this project has been a collaborative effort. For over a year, Atilla and Yuchen dedicated 20% of their time to working with Been Kim , Andrew Carroll and myself on this project. It has been a fun exploration!

Say hi if you see me.

DeepVariant 1.8 is out. Pangenome is here and it just got ~50% faster.

Release of DeepVariant and DeepSomatic v1.9 DV: Added training on HG002 T2T-Q100. Error reduction of 12% for Illumina and 30% for PacBio on this truth set. 25% faster. DeepTrio is 5x faster (20h -> 4h). DS: New models FFPE_TUMOR_ONLY for {WGS, WES}. Much improved WGS models.