Chilled snowboard day with the family

Fire and snow outside make for a perfect Sunday morning mood

Enjoying Frankfort and the IABS meeting for NGS in adventitious virus detection. Great conference so far

Enjoyed a quick morning run at the lake. Holds work problems again at bay

Heads up: This is an industry derived code and the license does not allow it's usage for profit

GitHub - ngs-ai-org/splitty: Tool suite around gene fusion detection and analysis Tool suite around gene fusion detection and analysis - ngs-ai-org/splitty

Just released our tool "splitty" github.com/ngs-ai-org/s... for fusion detection from transcripts. It's a BAM-based fusion caller in #rust for short- and long-reads, as well as tools around BND VCF entries (clustering, filtering,...).
Soon hopefully a publication with it's application will follow 🤞

Another very insightful paper on #methylation and long-read sequencing by @gangfang.bsky.social, describing some important but frequently overlooked caveats.

Gang provides a fantastic summary in his post, but here's my take too😅:

(1st post @BlueSky) Preprint alert🚨a long thread. Cautions in the use of @nanopore sequencing to map DNA modifications: officially reported “accuracy” ≠ reliable mapping in real applications. We performed a critical assessment of nanopore sequencing (across different versions of models) for the 1/n

PAPET: a collection of performant algorithms to identify 5-methyl cytosine from PacBio SequelII data CpGs methylation is an important feature for the regulation of gene expression in vertebreate genomes. In this paper, we present the PAcBio Predicting Epigenetics Toolkit (PAPET) algorithms. PAPET is ...

Great threat and highlighting a few critical points which we reflected internally on as well, when we analyzed methylation in PacBio data www.biorxiv.org/content/10.1...

GitHub - kcleal/superintervals: Fast interval intersection library Fast interval intersection library. Contribute to kcleal/superintervals development by creating an account on GitHub.

New interval lookup library just hit for Rust, C++ and Python — claims best in class performance! Pretty cool : github.com/kcleal/super...

Do you know how it compares in general to interval trees ? Both in speed and "usability" e.g. compared with rust bio interval trees? docs.rs/bio/latest/b...

Science break

Damn too late. Did they mention if they make recordings available?

Great work and intriguing story. I am glad that I could contribute a bit, too. #🧪

GitHub - sourmash-bio/sourmash: Quickly search, compare, and analyze genomic and metagenomic data se... Quickly search, compare, and analyze genomic and metagenomic data sets. - GitHub - sourmash-bio/sourmash: Quickly search, compare, and analyze genomic and metagenomic data sets.

So @ctitusbrown.bsky.social gave a talk for our Genome Center faculty meeting & I got reacquainted with sourmash -- github.com/sourmash-bio... really easy to install - got it to work in a few minutes on my laptop and desktop -- lots of interesting findings already ...

Thanks Titus et al.

Most large structural variants in cancer genomes can be detected without long reads - Nature Genetic... JaBbA v1 pinpoints the ‘loose ends’ of large (>10-kb) unmapped structural variants in short-read DNA sequencing, suggesting that about 90% of cancer chromosomal alterations outside centromeres ...

Bold claim!

www.nature.com/articles/s41...

Completely agree on that part 😉

I think unit testing is really a must have. CI sometimes becomes more tricky in my experience when meaningful results can only be obtained with large and heavy data.

Relaxing a bit after a demanding week

This is the dirty secret of the ctDNA field. The false positives will absolutely bankrupt the medical system if they're rolled out as is (not to mention the mental trauma!)

Blood tests for cancer may be useful someday, but the hype needs to be kept in check until the results are there.

Profiling Chromatin Accessibility in Humans Using Adenine Methylation and Long-Read Sequencing https://www.biorxiv.org/content/10.1101/2023.10.05.561129v1 Chromatin accessibility demonstrates accessible DNA regions that usually have regulatory function. S

Profiling Chromatin Accessibility in Humans Using Adenine Methylation and Long-Read Sequencing www.biorxiv.org/content/10.1101/2023.10....

Looking forward to read that one 👍🧪

Thx, I guess Nucleic Acid Research (methods), BMC or Plos Computational Biology might be good options. Any recommendations by chance?

Unfortunately Bioinformatics rejected our Pacbio methylation Algo manuscript www.biorxiv.org/content/10.1... . Reviews were constructive and easy to address, none questioned method itself, results or that it should be published. Strange.. off to the next publisher then 🧪

Getting slowly a hang on these intervals

Enjoyed a family weekend hike in the nearby mountains, Les Moss

Thrilled to see that the approach to which I contributed is going forward and might eventually help in the early detection of pancreatic cancer

blog.crownbio.com/a-novel-panc...

Announcing myself here with a genome announcement coming out of our group recently 🤗 academic.oup.com/g3journal/ad...

Reference genomes for BALB/c Nude and NOD/SCID mouse models