Jim Shaw
@jim_elevator
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Postdoc with Heng Li at Dana-Farber/Harvard Med School. Math PhD from @UofT with @YunWilliamYu. Working on methods for analyzing (metagenomic) sequencing data.
Joined April 2018
skani v0.3.0 is released. * 30-40% potential reduction in memory .* Breaking changes to indexing and searching databases. Calculate ANI for contigs, genomes. Search vs > 140k genomes: pre-indexed GTDB-R226 available for download.
github.com
Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs. - bluenote-1577/skani
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RT @yk_tani: I'm excited to share that I will soon join UCLA's Bioengineering department as an Assistant Professor. I am incredibly fortuna….
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RT @lh3lh3: Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling spl….
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RT @uthsavc: New life update! 🎆. 🎓 This Fall, I will be joining the Department of Computer Science at Johns Hopkins University (@JHUCompSci….
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RT @lh3lh3: @csuhuangneng developed longcallR for joint SNP calling and phasing from long RNA-seq reads, AND for identifying allele-specifi….
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I'm mostly active on bluesky nowadays, so see the bsky thread for more details:.
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RT @uthsavc: GASTON, our method to learn “topographic maps” of gene expression, is out now @naturemethods!. IMO the coolest part is a new m….
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RT @NiranjanTW: Tech Alert! 🚀🧬 We can now determine the sequence of DNA with non-canonical bases in a direct and high-throughput manner wit….
biorxiv.org
The discovery of synthetic xeno-nucleic acids (XNAs) that can basepair as unnatural bases (UBs) to expand the genetic alphabet has spawned interest in many applications, from synthetic biology to DNA...
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RT @ChengChhy: Hifiasm 0.21.0 has been released. It now has a beta module for direct assembly of ONT R10 simplex reads. Initial tests with….
github.com
Since Hifiasm-0.20.0 (r639): New Feature: Introduced a beta module for ONT assembly using ONT simplex R10 reads. To enable this feature, add the --ont option as shown below: hifiasm -t64 --ont -o...
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RT @chirgjain: Happy to see our method for T2T genome assembly published! It addresses an important limitation of string graph, that is, th….
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RT @li_chenhao: Just tried Sylph by @jim_elevator. Processed >2000 samples in a few hours on google cloud powered b….
github.com
ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash. - bluenote-1577/sylph
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RT @curious_coding: I gave a talk recently at Ben Langmead's group on my post on fast computation of random minimizers. Was super fun!. Blo….
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RT @KarelBrinda: A new paper from our amazing @sladky_on (jointly supervised with @VeselyPavel_mff) on super space-efficient indexing of ar….
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Lastly, thanks to users of sylph and those who have talked/messaged me about it. The referees were fair and helpful as well. New users, let me know how you find the software!. 5/5.
github.com
ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash. - bluenote-1577/sylph
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Secondly, apparently Oxford Nanopore (@oxfordnanopore) found that sylph was the most accurate metagenome profiler in their whitepaper. Very neat, and I didn't even find out about this until recently. 4/5.
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Firstly, the amazing AllTheBacteria team used sylph for QCing ~2 million isolate microbe assemblies using sylph! . A use case I didn't think about, but they found it worked well. 3/5.
First step in a community project to provide a uniformly assembled, annotated and searchable set of bacterial genomes, our preprint on our initial release of 1.9 million genome assemblies+taxonomic estimates. (figure compares with previous 661k dataset).
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I previously discussed sylph on Twitter; see the link below. I want to highlight a few new developments since then. 2/5.
Presenting sylph (, a fast, precise metagenomic profiler. Work done with @YunWilliamYu. sylph is highly accurate at the species level and takes ~1 minute and 16 GB RAM to profile against 85k prokaryotes and 2.9 million viral genomes. 1/10
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Happy to announce that our (me and @YunWilliamYu) metagenome profiler sylph ( is now published in @NatureBiotech! . 1/5.
github.com
ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash. - bluenote-1577/sylph
Rapid species-level metagenome profiling and containment estimation with sylph
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RT @lh3lh3: Published in 2009, bwa-aln is one of the oldest short-read aligners. It remains a popular choice for aligning ancient DNA reads….
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