SeqNextGen retweeted
There are so many intangible benefits supporting users of your open source #Bioinformatics, but at some point you have to get paid for it. The folks asking the questions are getting paid, so why not us?
SeqNextGen retweeted
pggb, the PanGenome Graph Builder, makes it easy to create pangenome graphs out of complete assemblies
SeqNextGen retweeted
I don't get it. The @humancellatlas project is organizing a meeting in July to "continue progress towards building the first draft of the Human Cell Atlas" (see events.humancellatlas.org/20…), but a first-draft human cell atlas was already published a year ago! statnews.com/2022/05/12/huma…
SeqNextGen retweeted
Bioinformaticians: which one(s) do you consider yourself?
• Molecular Biology Debugger
• Technical Leader
• Thought Leader
• Expert Executor
• Pragmatic Skeptic
• Trusted Teammate
#Bioinformatics #Hiring #Genomics @fulcrumgenomics
Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing | Nature Methods nature.com/articles/s41592-0…
SeqNextGen retweeted
LINX is finally published! cell.com/cell-genomics/fullt…. A🧵on some things I learnt from working on this.
SeqNextGen retweeted
Multiplex de Bruijn graphs enable genome assembly from long, high-fidelity reads go.nature.com/35bCOL1
SeqNextGen retweeted
bioRxiv now does not accept preprints on bioinformatics tools alone. If I have an announcement of a tool that I want to get out into the world right away, rather than in 6 months after it goes through peer review, what are some other options?
SeqNextGen retweeted
I spent six months analyzing data that took three days to generate and I think that’s fairly representative of my experience with the dry/wetlab ratio in single cell genomics
SeqNextGen retweeted
Excited to announce the *first* complete telomere-to-telomere assembly of a human autosome: chromosome 8! We resolved every gap in chromosome 8, including the centromere! biorxiv.org/content/10.1101/… #T2T
SeqNextGen retweeted
What do Eulerian and Hamiltonian cycles have to do with genome assembly? A blog post with Mihai Pop: medvedevgroup.com/2020/08/21…
SeqNextGen retweeted
Just read a cool paper (doi.org/10.1371/journal.pone… @burkhard_mstern). Main idea, as I extrapolate it: by measuring Jaccard at two values of k instead of 1, we can estimate ANI even if the sequences share a lot of non-homologous segments. Mash and similar tools fail in this case.
SeqNextGen retweeted
Write up from the @NSF on our tomato work! nsf.gov/discoveries/disc_sum…
SeqNextGen retweeted
I've been developing & teaching this GWAS course since 2009, but will not be teaching it anymore. Some of the material survived since 2009, some of it only appeared recently. Feel free to use anything, this link contains slides, literature, and practicals:
drive.google.com/file/d/1srS…
SeqNextGen retweeted
The President of @JohnsHopkins is an immigrant.
The Provost of @JohnsHopkins is an immigrant.
The VP for Research of @JohnsHopkins is an immigrant.
The Dean of Research of the @HopkinsMedNews is an immigrant.
The anti-immigrant Trump administration is hurting American science by @UshmaNeill link.medium.com/YKjjeget36
SeqNextGen retweeted
#SARSCoV2 pangenome made from 50 genomes in genbank. Top, graph viz and detail showing SNP bubbles. Middle: matrix view of genomes versus nodes in the graph. Bottom: genes versus the pangenome. CC @jervenbolleman @simonheumos @JosiahSeaman
SeqNextGen retweeted
Introducing Project 1000x1000: These are not normal times; we need new solutions. What if (big IF) 1000's of small businesses/fablab's could make specialized nano-materials for roughly 1000 to 10K N95 grade mask/day locally. 1000x1000 is a million mask/day produced locally. (2/n)
SeqNextGen retweeted
Code examples of fast and simple k-mer counters: github.com/lh3/kmer-cnt. The goal is to show how much engineering tricks can affect the performance and to provide a building block for k-mer counting.
