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Bede Constantinides

@bedec.bsky.social

900 followers 1.4K following 110 posts

Interested in infectious disease informatics. Research fellow at the University of Birmingham. Also cycling, photography, active travel. https://bede.im

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Bede Constantinides @bedec.bsky.social · Jun 13

New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search.
github.com/bede/deacon

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jun 13

Deacon: fast sequence filtering and contaminant depletion https://www.biorxiv.org/content/10.1101/2025.06.09.658732v1

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Reposted by Bede Constantinides

Ragnar {Groot Koerkamp} @curiouscoding.nl · 2h

So what's the equivalent of `perf record && perf report` on a MacBook?

I want to see the generated assembly and which lines are hot.

Reposted by Bede Constantinides

Adam Phillippy @aphillippy.bsky.social · 1d

Last week we were in the Washington Post for our characterization of Robertsonian chromosomes. This week we are entering our 10th day of being shut down and all of our research is on hold. To help me feel not-so-bad, here is a thread of some studies we released right before the shutdown 🧵 [1/n]...

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Reposted by Bede Constantinides

Adam Phillippy @aphillippy.bsky.social · 1d

Funny story, though, we found this gene in NCBI databases, but it was annotated in Streptococcus pneumoniae! This is surely human contamination in a bacterial strep sample that was not properly filtered. Lesson: use CHM13, or better yet a pangenome, when filtering for human contamination...

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Reposted by Bede Constantinides

Robert Aboukhalil @robert.bio · 1d

Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt

It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.

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Reposted by Bede Constantinides

Ben Langmead @benlangmead.bsky.social · 4d

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.

Burrows-Wheeler Indexing - YouTube

Videos on : (a) the Burrows-Wheeler Transform (BWT), (b) the FM Index, which uses the BWT to construct a full-text index, (c) Wheeler graphs, (d) r-index, an...

www.youtube.com

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Bede Constantinides @bedec.bsky.social · 3d

Yes I got the upload pings and almost posted the same here. A treasure trove of material.

Bede Constantinides @bedec.bsky.social · 3d

No harm in sticking with an old version :-) Results should be identical to 0.10.0 except for seqs containing IUPAC ambiguous bases, changing the classification of exactly one read in my IUPAC benchmark dataset.

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Bede Constantinides @bedec.bsky.social · 3d

Deacon 0.11.0:
- Local server mode
- Ultra-careful handling of non-ACGT
- Faster indexing & index loading
- Denser index now stores k-mers not hashes
- xxHash & FxHash replaced with rapidhash::fast
- Bug fixes

Thanks @curiouscoding.nl (and others!) for contributions
github.com/bede/deacon/...

Release 0.11.0 · bede/deacon

Major release incorporating new features, fixes and peformance optimisations. Includes many PRs from @RagnarGrootKoerkamp, taking advantage of new features in simd-minimizers, packed-seq and parase...

github.com

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Bede Constantinides @bedec.bsky.social · 4d

I had a quick look but was intimidated by the docs honestly. Nick from the Zstd team mentioned BAMs wrt a forthcoming post on use cases, so hopefully we'll soon have some diverse profiles to learn from. news.ycombinator.com/item?id=4549...

Do you happen to have a pointer to a good open source dataset to look at? Naivel... | Hacker News

news.ycombinator.com

Bede Constantinides @bedec.bsky.social · 4d

Nick Terrell (Meta): "Looking at the BAM format, it looks like the tokenization portion will be easy. Which means I can focus on the compression side, which is more interesting."

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Bede Constantinides @bedec.bsky.social · 4d

It doesn't compress e.g. FASTA out of the box currently. The bundled profiles are geared towards sensible fixed-length formats like Parquet. I imagine we'll see new profiles emerge quickly openzl.org/getting-star...

Quick Start - OpenZL

openzl.org

Bede Constantinides @bedec.bsky.social · 4d

"It was really hard to resist spilling the beans about OpenZL on this recent HN post about compressing genomic sequence data"
news.ycombinator.com/item?id=4549...

It was really hard to resist spilling the beans about OpenZL on this recent HN p... | Hacker News

news.ycombinator.com

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Bede Constantinides @bedec.bsky.social · 4d

"OpenZL is our answer to the tension between the performance of format-specific compressors and the maintenance simplicity of a single executable binary."
engineering.fb.com/2025/10/06/d...

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Bede Constantinides @bedec.bsky.social · 5d

Oh it's a pity if splitting into crates is punished with much worse compile times. Is this the case?

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Bede Constantinides @bedec.bsky.social · 5d

Fun question! Doubt it would noticeably change the plot though. Gzip's 32KB window is a tiny fraction of genome length for anything larger than a virus. Would compress low complexity regions well but miss e.g. gene duplications.

Bede Constantinides @bedec.bsky.social · 9d

I can't bring myself to bet against HashSet given recent experience

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Reposted by Bede Constantinides

Ragnar {Groot Koerkamp} @curiouscoding.nl · 10d

Looking for people to test the latest version of simd-sketch.

It's now 2x as fast at sketching, and supports skipping over kmers containing N and other ambiguous bases (which is only ~35% slower).

'cargo install simd-sketch' is right there under your fingertips ;)

github.com/RagnarGrootK...

GitHub - RagnarGrootKoerkamp/simd-sketch: Compute bottom-s sketches and s-buckets sketches, using simd-minimizers crate.

Compute bottom-s sketches and s-buckets sketches, using simd-minimizers crate. - RagnarGrootKoerkamp/simd-sketch

github.com

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Reposted by Bede Constantinides

Ragnar {Groot Koerkamp} @curiouscoding.nl · 12d

FxHashSet::<u32>::contains throughput is wild!

- Up to 4x slowdown for negative queries due to probing.
- Positive queries are fast for small tables, but slow in RAM because they need 2 cache misses.

Lots of variance depending on the load factor, ie whether n is close to 87.5% of a power of 2.

Plot of (inverse) throughput of querying an FxHashSet<u32> of increasing size. 3 lines show the throughput when 1%, 50%, or 99% of queries is present in the set. The 1% and 50% lines show big spikes just before every power of 2, where they are up to 3x slower than in the best case.

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Reposted by Bede Constantinides

Dorottya Nagy @dotnagy.bsky.social · 16d

Pleased to see this pre-printed, highlighting the completeness/accuracy of @nanoporetech.com long-read genome assembly for clinical Enterobacterales: www.biorxiv.org/content/10.1...

Thanks to colleagues @modmedmicro.bsky.social, @ukhsa.bsky.social, @genewiz.bsky.social and @oxfordbrc.bsky.social!

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Reposted by Bede Constantinides

Nick Loman @pathogenomenick.bsky.social · 22d

Terrific new feature presented by @theo.io on @pathoplexus.org called SeqSets for generating DOIs for sequence subsets used in publications, that can then be tracked for impact via CrossRef that will allow data generators to track impact! #IMMEMXiV

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Bede Constantinides @bedec.bsky.social · 25d

Thanks! Had assumed there'd be a good reason…

Bede Constantinides @bedec.bsky.social · 25d

Oh I didn't know 2bit supported Ns through extra data blocks. I wonder how easily it can be parsed in parallel compared to Binseq – perhaps @noamteyssier.bsky.social can comment?

Bede Constantinides @bedec.bsky.social · 25d

Some applications do need that 5th symbol to represent ambiguity / N, which I assume is why BAM uses 4bit encoding (IIRC). 2bit + bit mask(s) is another way to do it.

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Bede Constantinides @bedec.bsky.social · 26d

Predictably the comments section is mostly horror at the state of FASTA format

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Bede Constantinides @bedec.bsky.social · 26d

Front page of Hacker News 🫨
bsky.app/profile/bede...

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