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Reposted by Jim Shaw

Roland Faure @rfaure.bsky.social · 4d

Our preprint on our new metagenomic HiFi assembler Alice is out 🥳 Based on a *new sketching method* (🧵1/6)
👉 Preprint www.biorxiv.org/content/10.1...
👉 Github github.com/rolandfaure/...

Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching

We introduce Mapping-friendly Sequence Reduction (MSR) sketches, a sketching method for high-fidelity (HiFi) long reads, and Alice, an assembler that operates directly on these sketches. MSR produces ...

www.biorxiv.org

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Reposted by Jim Shaw

Dan Portik @dportik.bsky.social · 6d

New pre-print from the Banfield lab, highlighting an interesting case of 1.5Mb megaplasmids found in human gut.

Plasmid genomes were resolved using #PacBio HiFi sequencing with hifiasm-meta for #metagenome assembly. Host association was detected using epigenetic signals.

doi.org/10.1101/2025...

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae

Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplas...

doi.org

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Reposted by Jim Shaw

Heng Li @lh3lh3.bsky.social · 8d

Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/o.... Work with Alvin Qin

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Reposted by Jim Shaw

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 8d

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV https://www.biorxiv.org/content/10.1101/2025.09.26.678787v1

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Reposted by Jim Shaw

Zamin Iqbal @zaminiqbal.bsky.social · 12d

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n

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Jim Shaw @jimshaw.bsky.social · 15d

Super classy and much respect for updating the benchmarks Ryan. What a nice surprise. Very appreciated as a developer :).

Grats on the huge improvements @gaetanbenoit.bsky.social for metamdbg

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Reposted by Jim Shaw

Ryan Wick @rrwick.bsky.social · 15d

New blog post!

metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper:
rrwick.github.io/2025/09/23/a...

Both tools improved considerably! Time to update your conda environments 😄

Benchmark update: metaMDBG and Myloasm

a blog for miscellaneous bioinformatics stuff

rrwick.github.io

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Reposted by Jim Shaw

Samuel King @samuelhking.bsky.social · 20d

Many of the most complex and useful functions in biology emerge at the scale of whole genomes.

Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵

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Reposted by Jim Shaw

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 21d

agtools: a software framework to manipulate assembly graphs https://www.biorxiv.org/content/10.1101/2025.09.14.676178v1

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Reposted by Jim Shaw

AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 23d

X-Mapper 🦠🧬🧪 - a sequence aligner developed for microbes, now on Bioconda! 🚀
• 11–24× fewer suboptimal alignments (same for human genome)
• 3–579× lower inconsistency
• improves on ~30% of reads aligned to non-target species
github.com/mathjeff/map...
bioconda.github.io/recipes/x-ma...
#microsky

Alignment algorithms represent a balance between speed and accuracy. We evaluated this balance across aligners, with accuracy measured by suboptimal alignments. We found that the relationship between alignment time (with 30 threads) and suboptimal alignment rates exhibits diminishing returns, where X-Mapper stands out as an outlier, offering the highest accuracy with competitive speed.

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Reposted by Jim Shaw

Heng Li @lh3lh3.bsky.social · 26d

New blog post – A quick look at Roche's SBX
lh3.github.io/2025/09/11/a...

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Jim Shaw @jimshaw.bsky.social · 27d

Great!! Let me know what you find :)

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Reposted by Jim Shaw

Wei Shen 沈伟 @shenwei356.bsky.social · 28d

I sincerely appreciate the opportunity to visit @ebi.embl.org (thanks to the @embl.org Sabbatical fellowship). The guidance and support I received from Zam (@zaminiqbal.bsky.social), John (@bacpop.org) and other colleagues have been immensely valuable! You changed my career！❤️

Zamin Iqbal @zaminiqbal.bsky.social · 28d

Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology

LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

www.nature.com

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Reposted by Jim Shaw

Zamin Iqbal @zaminiqbal.bsky.social · 28d

Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology

LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

www.nature.com

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Reposted by Jim Shaw

Heng Li @lh3lh3.bsky.social · 28d

Now preprinted at arxiv.org/abs/2509.07357

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Reposted by Jim Shaw

Falk Hildebrand @bioinf.bsky.social · 28d

How do you long-read sequence metagenomes? I would argue it starts with the right sample storage & DNA extraction, to enable efficient @nanoporetech.com /@pacbio.bsky.social sequencing, which we investigated in our new paper: www.biorxiv.org/content/10.1...

Massive thanks to Klara for driving this

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Jim Shaw @jimshaw.bsky.social · 29d

Not included with myloasm, but check out pubmed.ncbi.nlm.nih.gov/38833287/ maybe?

How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies - PubMed

It is now possible to assemble near-perfect bacterial genomes using Oxford Nanopore Technologies (ONT) long reads, but short-read polishing is usually required for perfection. However, the effect of s...

pubmed.ncbi.nlm.nih.gov

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Jim Shaw @jimshaw.bsky.social · 29d

Thanks Sergey!!

Jim Shaw @jimshaw.bsky.social · 29d

Indeed! Thanks @usadellab.bsky.social

Jim Shaw @jimshaw.bsky.social · Sep 8

Thanks @shenwei356.bsky.social !

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Jim Shaw @jimshaw.bsky.social · Sep 7

Thanks to co-authors @lh3lh3.bsky.social @mgmarin.bsky.social and the Heng Li lab here in Dana-Farber / Harvard Med.

Much thanks to all folks who generate/deposit data.

Building an assembler from scratch has always been a goal of mine, a labour of love :).

github.com/bluenote-157...

END

GitHub - bluenote-1577/myloasm: A new high-resolution long-read metagenome assembler for even noisy reads

A new high-resolution long-read metagenome assembler for even noisy reads - bluenote-1577/myloasm

github.com

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Jim Shaw @jimshaw.bsky.social · Sep 7

In conclusion:

1. Check out our new long-read metagenome assembler github.com/bluenote-157.... It's written from scratch, in rust!

2. Myloasm excels on ONT R10.4 data, but works for HiFi too

3. I'm really excited by its ability to enable high-resolution sleuthing for microbiome genomics

11 / N

GitHub - bluenote-1577/myloasm: A new high-resolution long-read metagenome assembler for even noisy reads

A new high-resolution long-read metagenome assembler for even noisy reads - bluenote-1577/myloasm

github.com

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Jim Shaw @jimshaw.bsky.social · Sep 7

On a public oral ONT metagenome (from @ykiguchi.bsky.social), we assembled a lot more complete, similar (within species-level) genomes than previous methods.

So much to explore... for example, we compared 6 circular TM7 bacteria of > 93% ANI assembled from a single oral metagenome.

10 / N

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Jim Shaw @jimshaw.bsky.social · Sep 7

For this gut sample, @mgmarin.bsky.social found two distinct ermF (erythromycin resistance) genes, with 98% similarity, spreading within Bacteroidota.

1. The distinct ermFs are spreading on two distinct MGEs.
2. There is even strain specificity, only 1/6 P. copri had it!

9 / N

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Jim Shaw @jimshaw.bsky.social · Sep 7

With circular contigs, we can confidently analyze presence / absence of "stuff" within contigs _without worrying about binning issues_ (as much).

For example, mobile genetic elements, AMR genes that are hard to bin and assemble with short reads...?

8/N

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