Jim Shaw
@jimshaw.bsky.social
Postdoc at Dana-Farber and Harvard Med with Heng Li (@lh3lh3.bsky.social). Prev: UBC / UofT.
I like thinking about computational biological sequence analysis and its applications to metagenomics.
https://jim-shaw-bluenote.github.io
I like thinking about computational biological sequence analysis and its applications to metagenomics.
https://jim-shaw-bluenote.github.io
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
Grats on the huge improvements @gaetanbenoit.bsky.social for metamdbg
September 23, 2025 at 1:15 PM
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
Grats on the huge improvements @gaetanbenoit.bsky.social for metamdbg
Great!! Let me know what you find :)
September 11, 2025 at 12:43 PM
Great!! Let me know what you find :)
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
September 8, 2025 at 4:37 PM
Not included with myloasm, but check out pubmed.ncbi.nlm.nih.gov/38833287/ maybe?
Indeed! Thanks @usadellab.bsky.social
September 8, 2025 at 4:36 PM
Indeed! Thanks @usadellab.bsky.social
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
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
September 7, 2025 at 11:35 PM
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
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
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
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
September 7, 2025 at 11:35 PM
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
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