Accompanied by a less polished nextflow pipeline to handle multiple samples and pre-processing - github.com/allydunham/d.... Configurably downsample, merge and trim reads before quantification plus FastQC, SeqKit Stats and a quanitification QC plot. Inspired by the github.com/cancerit/QUA....

I have more features planned to support my work, for instance multiple constructs in one library, combinations of sub-libraries and a region type expecting variants to a base sequence, but issues and pull-requests with other bugs and suggestions are very welcome too.

Simulated tests and benchmarks and our datasets suggest the tool is generally accurate and robust as well as pretty quick. Feels like a state that could be useful more widely so a good time to share, although I do expect more bugs to come out with wider usage!

Currently position in reads, flanking patterns and full alignment can be used to extract regions and extact matching, hamming distance and (bounded) Levenshtein used to compare to your library. This lets you nicely balance match accuracy with speed for your design.

It takes in (paired) fastq/a files, a JSON expected read structure, an optional expected combinations TSV and a strategy for extracting and matching variable regions and outputs count tables against your library.

We've been screening across many DNA construct structures with variable number/size of interesting regions - e.g. spacer, extension and barcode for prime editing. There wasn't a widely used tool to process these complex structured reads so I ended up developing github.com/allydunham/d....

MPRAbase (mprabase.ucsf.edu) , a customized database for massively parallel reporter assays (MPRAs) to easily find and download MPRA data. Amazing work by Jingjing Zhao, Fotis Baltoumas, Georgios Pavlopoulos, @vagar.bsky.social, ilias Georgakopoulos-Soares & others.

genome.cshlp.org/content/earl...

We're hiring to expand on the work to understand the human genome by engineering it!
lnkd.in/da-gitNc

We are happy to share our enhancer scramble story, a strategy to create hundreds of stochastic deletions, inversions, and duplications within mammalian gene regulatory regions and associate these new architectures with gene expression levels 🧵
www.biorxiv.org/content/10.1...

Does my mutation have the same impact as yours? Population genetics 🤠 🥸 🤓 🤡 meets single cell CRISPRi ⚡ ! www.biorxiv.org/content/10.1... Led by Claudia Feng, Oliver Stegle, Britta Velten, @sangerinstitute.bsky.social .