1/7 Very interesting blog by Broad Clinical Labs about CNV call. Recently, I add code in PGR-TK (dev main branch) to call small variants & structural variant candidates with a PGR-TK internal whole genome aligner. #genomics #sequencing broadclinicallabs.org/seeking-truth-…

You could also generate stratification BED files for your assembly or reference github.com/ndwarshuis/gia… A great team work led by Justin Zook and Nathan Dwarshuis Genome in a Bottle with Jennifer McDaniel, Divya Kalra, Ben Busby!, Nathan Olson, Justin Wagner, Fritz Sedlazeck &others

A review on tandem repeats and disease by Arvis Sulovari Danny E. Miller MD PhD Paul Valdmanis EEE and myself is up online at doi.org/10.1042/ETLS20… . As far as I know, Danny's table of repeat-associated diseases is the most comprehensive published to date.

There is now PacBio Kinnex (shown as MAS-Seq) RNA data from GIAB!

Tandem repeats are hard! Get your benchmark from Genome in a Bottle: biorxiv.org/content/10.110… 1.7 mil TR catalog; new tooling to overcome variant representation issues (SNV &SV); insight in complexity First time we can compare across different techs/caller! BCM HGSC Rice Computer Science

In 2023, one of my goals was to provide a new utility for calling diploid variations (SNP + SVs) from diploid genome assemblies more efficiently. I am happy that I have finished the code before the end of 2023. It is a nice closure for something I liked to finish for a while.

Has anyone made a Genome in a Bottle joke yet? nature.com/articles/s4200… Genome in a Bottle #GIAB

We are proud to announce a new hg38 track group consisting of Human Pangenome Reference Consortium data. In this first release, there are tracks displaying features and variations of HPRC results compared to hg38, as well as alignment tracks. See the full announcement: bit.ly/HPRCdataInUCSC…

New vcfdist paper on bioRxiv! Key Takeaways: 1) Jointly evaluating small and structural variants decreases measured FN+FP by 20-50% 2) 43-92% of phasing flip "errors" are FP due to variant representations More below Code: github.com/TimD1/vcfdist Paper: biorxiv.org/content/10.110…

Thank you Director Green! BioDIGS has truly been a highlight of my career. It starts with collecting soil from all over the United States and then diving deep into the informatics to study the genomic diversity of the world around us. schatz-lab.org/presentations/…

Preprint on Exploring gene content with pangenome gene graphs: arxiv.org/abs/2402.16185. It describes pangene for building gene graphs and for calling gene-level variations which can be found at pangene.bioinweb.org. Pleasant collaboration with Maximillian Marin and Maha Farhat.

Two other resources of note for IGV: - Interactive guide to getting started with IGV: sandbox.bio/tutorials/igv-… - The supplement to this article, which is an incredibly comprehensive visual guide to reviewing somatic variants: ncbi.nlm.nih.gov/pmc/articles/P…

Our 10th LR seminar BCM HGSC at 22nd March 10am CT! Come join us and listen to new advancements on LR from Miten Jain Tychele Turner Genome in a Bottle Vanessa Porter, PhD Register: hgsc.bcm.edu/LongReadSeminar BCMHouston BCM Department of Molecular and Human Genetics PacBio Oxford Nanopore Rice Computer Science Texas Medical Center⁩

SplitThreader, my cancer SV viz tool, is 8 years old. I have some ideas for giving it a makeover that would make it much more lightweight and easy to prepare input files for. Please reply if you are interested so I can tell if I should prioritize this! splitthreader.com/vis.php?code=e…

Want to learn more about the tricks and tips for generating ONT Ultra-long DNA? The T2T Consortium and UCSC SeqTech Center are hosting a Technology-focused Webinar next Thursday with a group of experts. Register today: bit.ly/3PFTa2f Adam Phillippy

Tandem repeat Genome in a Bottle benchmark Nature Biotechnology out today: rdcu.be/dFQNN . Characterization of 1.7 million TR + benchmark variants + new method to overcome var. representation issues! Great work lead by Adam E. BCM HGSC & great collab. from so many! (1/4)

📢 By popular demand, you can now add tracks to IGV Desktop directly from 42basepairs!