Shane McCarthy

478 posts

Shane McCarthy

Shane McCarthy

@mcshane

Assembler of genomes for the Tree of Life programme at Wellcome Sanger. Ex-physicist. Sandgroper

Cambridge, UK Katılım Mart 2007
462 Takip Edilen637 Takipçiler
Shane McCarthy retweetledi
Tom Mathers @tom-mathers.bsky.social
Tom Mathers @tom-mathers.bsky.social@Thomas_Mathers·
Working on a very cool @darwintreelife assembly today. Haplotype resolved assembly of PENTAPLOID Rosa agrestis. They have asymetric meiosis with two chroms forming bivalents and the other three inherited as univalents through the egg. Spot the bivalent pairs in the HIC map.
Tom Mathers @tom-mathers.bsky.social tweet mediaTom Mathers @tom-mathers.bsky.social tweet media
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Regev Schweiger
Regev Schweiger@RegevSchweiger·
Our new preprint is up - “Insights into non-crossover recombination from long-read sperm sequencing”! biorxiv.org/content/10.110… Thread: 1/
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Shane McCarthy retweetledi
Tom Mathers @tom-mathers.bsky.social
Tom Mathers @tom-mathers.bsky.social@Thomas_Mathers·
Interesting #AssemblyCuration today @SangerToL. HiC-phased diploid assembly of a dragonfly. Curating both haplotypes together in a merged map. Pics show X and Y sex chromosomes that were mashed up between the haps and also lots of false duplication by hifiasm to be removed. 🧵
Tom Mathers @tom-mathers.bsky.social tweet mediaTom Mathers @tom-mathers.bsky.social tweet media
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Shane McCarthy retweetledi
Zamin Iqbal
Zamin Iqbal@ZaminIqbal·
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) biorxiv.org/content/10.110…
Zamin Iqbal tweet media
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Shane McCarthy retweetledi
Zamin Iqbal
Zamin Iqbal@ZaminIqbal·
Delighted this is out, led by @bricoletc , culmination of 10 yrs of work,started by Sorina Maciuca. New genome graph methods took a lot of work, but paid off, and Brice showed gene conversion between genes explained unusually deeply diverged lineages in 2 surface antigen genes.
PLOS Biology@PLOSBiology

Why do the #malaria parasite's #merozoite surface proteins #MSPs have exactly 2 deeply-diverged lineages? Genomic analysis of #Plasmodium DBLMSP & DBLMSP2 reveals the evolutionary explanation to this long-standing puzzle @bricoletc @ZaminIqbal #PLOSBiology plos.io/3TC8WOl

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Shane McCarthy retweetledi
Marcela Uliano-Silva
Marcela Uliano-Silva@MahUliano·
I worked in Shane's team for 4 years. They were some of the best years of my life. One of the positions is to replace me. Our DToL project is wonderful. I'm still in the project, just in another position now. Apply today! @darwintreelife
Shane McCarthy@mcshane

We have three positions open in the Tree of Life Assembly team @sangerinstitute @SangerToL working on biodiversity genome assembly for @darwintreelife, @erga_biodiv, @genomeark, @EBPgenome.

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Shane McCarthy
Shane McCarthy@mcshane·
We're also seeking a Principal Computer Scientist - someone to lead on algorithm and method development for genome assembly - so many challenges still remain from polyploids, to very large genomes, and complex symbiotic mixtures (tinyurl.com/tola-principal…). Come join us!
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Shane McCarthy
Shane McCarthy@mcshane·
There are two senior/bioinformatician roles to work on genome assembly, data analysis and the development of methods and software to support assembling genomes across diverse taxa from the Tree of Life (tinyurl.com/tola-bioinf24-…).
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Marko Prous
Marko Prous@mprous1·
@StevenFalk1 @nature_spotter do you know who to contact in the Darwin ToL consortium about DNA extractions? I tried MagAttract kit for 2 sawfly samples but got practically no DNA. I wonder if there's smth that you do differently using the same kit to get your sawfly genomes
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Shane McCarthy retweetledi
Karen Livesey
Karen Livesey@KarenLLivesey·
I've been dying to tell you all! I'm going on a national tour in 2023 representing the Australian Institute of Physics @ausphysics Looking forward to meeting lots of people as the Women in Physics lecturer. aip.org.au/News/13010152
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Shane McCarthy retweetledi
Erik Garrison
Erik Garrison@erikgarrison·
Safely sharing non-identifiable sequences from private cohorts of complete genome assemblies: privvg.github.io/2022/09/24/pra… (Or: How to build a global pangenome from siloed data)
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Keşfet

@darwintreelife @rajivmccoy @khmiga @EimearEKenny @aylwyn_scally @richard_durbin @bricoletc @sangerinstitute