I second the *supposed* part. I have been using so far for only mundane scripts but damn it is powerful.
12.02.2026 04:48
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I second the *supposed* part. I have been using so far for only mundane scripts but damn it is powerful.
Getting to the goal of one ecosystem to rule them all
Great if you have sometime, let’s catch up
Are you in San Diego?
I've added 7 videos to my Burrows-Wheeler indexing playlist (www.youtube.com/playlist?lis...), rounding out the r-index series and adding a 5-part series on the move structure. Now 27 videos in that playlist. I aim to add videos on prefix-free parsing, PBWT, Wheeler languages/automata in the future.
Oh yes you are right, this is the new corrected de Bruijn graph …..
at the end, the name made me the happiest lol.
The Genome Informatics conference (@ Cold Spring Harbor Lab, Nov 5 - 8) abstract deadline is **today**. We welcome your submissions! Topics include:
- PanGenomes
- Genome Assembly & Seq. Algos.
- Algorithmic Evo. Bio
- Single Cell & Spatial Omics
- Microbial Genomics
- AI/ML & Integrative Omics
🙏🙏🙏
Thanks @mikelove.bsky.social
So excited that this is finally out. This was among the longest and most uncertain (no)pun intended during my PhD, with different challenges, starting my from evaluation metrics to finding the right datasets, to tweak the method and interpreting the results.
github.com/NPSDC/mehenDi
The 25th iteration of the excellent Conference for Algorithms in Bioinformatics (WABI) starts tomorrow at UMD @umdscience.bsky.social at the Brendan Iribe Center. You can find details at the website wabiconf.github.io/2025/. We'll use the tag #WABI25 for the meeting!
🧬🖥️ oarfish v0.9.0 is out! The big improvement in this version is future-oriented. v0.9.0 allows the user to pass in transcript sequences via the `--annotated` option, the `--novel` option, or both. The provenance will be separately tracked to that later 1/4
🖥️🧬 The new release (v0.13.0) of piscem is out. However, almost all changes here are transparent to the user (except for the need to rebuild the index before using the new version). I want to take a second to talk about something that often goes unappreciated. 1/x
github.com/COMBINE-lab/...
A preprint by @elembio.bsky.social on an on flowcell simplified hybrid capture approach that retains high specificity and enables PCR-free workflow www.biorxiv.org/content/10.1...
@mikelove.bsky.social it's been a pleasure and an insightful experience collaborating with you. Thank you for taking out the time to attend my defense.
Excited and nervous at the time!!! Looking forward to it.
We just released simpleaf v0.19.0 (github.com/COMBINE-lab/...). Make sure to pair it with piscem v0.12 for faster scATAC-seq processing. The other big feature & first explicit @scverse.bsky.social integration point is AnnData format output with the new `--anndata-out` flag!
Very excited to see Movi (by @mohsenzakeri.bsky.social) now out in iScience: www.cell.com/iscience/ful.... Movi builds on the "move structure" pangenome index, a compressed full-text index and close cousin to r-index. Compared to r-index, the move structure is simpler and more cache-efficient.
It should definitely be doable if we store the rank and then we can perhaps later use it in the augmented bed file. We currently do support a SAM file as an output for the mappings for all the reads in the fastqs but then that does not do any deduplication/barcode correction.