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Wei Shen 沈伟

@shenwei356.bsky.social

2.3K followers 940 following 27 posts

Associate professor of Bioinformatics at Chongqing Medical University, China. Lab: https://mbio.info Personal: http://shenwei.me/ http://shenwei356.bsky.social

mbio.info

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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 Wei Shen 沈伟

EMBL-EBI @ebi.embl.org · 8d

There are millions of openly available microbial genomes, but searching them can be slow.

Until now 🥁

Introducing LexicMap, a new alignment tool that lets scientists search these data in minutes, helping track antibiotic resistance, trace outbreaks, and more.

www.ebi.ac.uk/about/news/r...
🦠

How to rapidly search the world’s microbial DNA

By making the world’s microbial DNA easier to explore, LexicMap helps researchers track outbreaks, study antibiotic resistance, and understand microbial diversity.

www.ebi.ac.uk

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Reposted by Wei Shen 沈伟

Paul Medvedev @pashadag.bsky.social · 13d

Thank you folks for your feedback on our survey about Hash functions in genomic sequence analysis. We've updated the paper and you can see the new version here: tinyurl.com/4kk9ccmt.

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Reposted by Wei Shen 沈伟

Zamin Iqbal @zaminiqbal.bsky.social · 13d

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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Wei Shen 沈伟 @shenwei356.bsky.social · 27d

I think it's because there are only a few bioinformatics packages to use. Most people don't want to reinvent wheels like me 😅

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Wei Shen 沈伟 @shenwei356.bsky.social · 27d

Glad you like them!

Reposted by Wei Shen 沈伟

Nature Biotechnology @natbiotech.nature.com · 28d

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - @shenwei356.bsky.social @zaminiqbal.bsky.social go.nature.com/3K09TgJ

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.

go.nature.com

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

BTW, we've just released v0.8.0, with reduced indexing and searching memory usage, more features (e.g., limiting search by TaxId), and more utilities to improve the usability.
github.com/shenwei356/L...

Release LexicMap v0.8.0 · shenwei356/LexicMap

v0.8.0 - 2025-09-10 No changes to the index format (see Index format changelog). New commands: lexicmap utils merge-search-results: Merge a query's search results from multiple indexes. lexicmap ...

github.com

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

Thanks!

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

Zamin Iqbal @zaminiqbal.bsky.social · 28d

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 Wei Shen 沈伟

Rob Patro @robp.bsky.social · Sep 8

Hashing vs. sorting; interesting! reiner.org/hashed-sorting. Also I wonder if, depending on your use case, semi-sorting provides an even greater benefit? 🧬🖥️

Hashed sorting is typically faster than hash tables

Benchmarks and theoretical explanation of why and when hashed radix sort beats hash tables.

reiner.org

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Wei Shen 沈伟 @shenwei356.bsky.social · Sep 8

Amazing Jim!

Jim Shaw @jimshaw.bsky.social · Sep 7

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!

Nanopore's getting accurate, but

1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?

with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social

1 / N

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Sep 7

High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1

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Reposted by Wei Shen 沈伟

Zamin Iqbal @zaminiqbal.bsky.social · Sep 4

Ok this is mad
"...an ant that lays individuals from two distinct species. In this life cycle, females must clone males of another species because they require their sperm to produce the worker caste"

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

One mother for two species via obligate cross-species cloning in ants - Nature

In a case of obligate cross-species cloning, female ants of Messor ibericus need to clone males of Messor structor to obtain sperm for producing the worker caste, resulting in males from the same moth...

www.nature.com

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Reposted by Wei Shen 沈伟

Rayan Chikhi @rayanchikhi.bsky.social · Sep 3

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024...

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Wei Shen 沈伟 @shenwei356.bsky.social · Aug 26

So amazed at how productive you were in 4 or 5 years, with so much great work!

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Reposted by Wei Shen 沈伟

Ragnar {Groot Koerkamp} @curiouscoding.nl · Aug 26

Finally printed and submitted my thesis :)

You may call me Dr. now 🎓

curiouscoding.nl/thesis.pdf

Picture of my printed thesis: Optimal Throughput Bioinformatics

With a cover image depicting increasingly more efficient pairwise alignment algorithms.

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Reposted by Wei Shen 沈伟

Michael Kuhn @biocs.bsky.social · Aug 15

We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7

#microsky

Metalog

Metalog is a repository of manually annotated metadata (or contextual data) for metagenomic sequencing data from across the globe.

metalog.embl.de

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Reposted by Wei Shen 沈伟

Zamin Iqbal @zaminiqbal.bsky.social · May 19

Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well
www.biorxiv.org/content/10.1...

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Wei Shen 沈伟 @shenwei356.bsky.social · May 6

TaxonKit v0.20.0 is adapted to recent rank changes in NCBI Taxonomy.
github.com/shenwei356/t...

Also updated
- taxid-changelog to May, 2025 github.com/shenwei356/t...
- gtdb-taxdump to GTDB r226 github.com/shenwei356/g...
- ictv-taxdump to VMR_MSL40 github.com/shenwei356/i...

Release TaxonKit v0.20.0 · shenwei356/taxonkit

Changes TaxonKit v0.20.0 This version is mainly for maintaining compatibility with NCBI's recent changes(1, 2). Please remove the ranks.txt file in ~/.taxonkit/ or other directories containing t...

github.com

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Wei Shen 沈伟 @shenwei356.bsky.social · Apr 14

⚡️LexicMap v0.7.0 fixed a minor bug in index building and improved the alignment accuracy!

Please rebuild the existing index. Sorry for the inconvenience. 🥹

github.com/shenwei356/L...

Release LexicMap v0.7.0 · shenwei356/LexicMap

v0.7.0 - 2025-04-11 Please rebuild the index, as some seeds in the genome end regions were missed during computation. lexicmap index: Fix a little bug in seed desert filling -- forgot to fill the...

github.com

Wei Shen 沈伟 @shenwei356.bsky.social · Mar 25

Ah! Do you mean that there would be a large number of seed matches, which bring too many candidates to check.

LexicMap returns anchors from 15-31 bp, so it can have a high specificity with fewer candidates to match when choosing the top chains. But by default, it checks all chains for sensitivity.

Wei Shen 沈伟 @shenwei356.bsky.social · Mar 25

Besides, Minimap2 is mainly designed for a few ref genomes with higher throughput. While LexicMap emphasizes scalability (million-scale ref genomes) and it's faster with a few queries. We've added Minimap2 and other tools in our benchmarks, which will be public in a few weeks.

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Wei Shen 沈伟 @shenwei356.bsky.social · Mar 25

Sorry, I didn't get the point of "avoid having too many 19-mers".

The biggest difference is that LexicMap's seeds support variable-length (prefix or suffix) matching, rather than exact match in tools such as Minimap2. But Minimap is more tolerant of mutations than LexicMap as it has denser seeds.

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Wei Shen 沈伟 @shenwei356.bsky.social · Mar 25

🚀 LexicMap v0.6.0 is released!
✅ More accurate alignments!
🎯 Higher sensitivity for short queries (>100bp)!
💡 Denser seeds, same index size!

🔬 Function: Efficient sequence alignment against millions of prokaryotic genomes!
📖 Docs: bioinf.shenwei.me/LexicMap/

Release LexicMap v0.6.0 · shenwei356/LexicMap

v0.6.0 - 2025-03-25 This version is compatible with indexes created by previous versions (requires a one-time, automatic preprocessing), but rebuilding the index is recommended for more accurate re...

github.com

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Wei Shen 沈伟 @shenwei356.bsky.social · Mar 24

Thrilled to finally debut my lab site🎉: mbio.info — which stands for Microbial Bioinformatics, a domain I purchased 9 years ago and has been waiting for this moment ever since!"

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Wei Shen 沈伟 @shenwei356.bsky.social · Mar 12

Just updated seqkit, csvtk, taxonkit, and rush.

Click to see changes:
- github.com/shenwei356/s...
- github.com/shenwei356/t...
- github.com/shenwei356/c...
- github.com/shenwei356/r...

Release SeqKit v2.10.0 · shenwei356/seqkit

Changes SeqKit v2.10.0 - 2025-03-12 seqkit: add a global flag --skip-file-check: skip input file checking when given a file list if you believe these files do exist. It helps to reduce file che...

github.com

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