Assembler of genomes for the Tree of Life programme at Wellcome Sanger. Ex-physicist. Sandgroper
Cambridge, UK
Joined March 2007
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Shane McCarthy retweeted
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.
Shane McCarthy retweeted
Our new preprint is up - “Insights into non-crossover recombination from long-read sperm sequencing”!
biorxiv.org/content/10.1101/… Thread: 1/
Shane McCarthy retweeted
Here's a thread about our new preprint biorxiv.org/content/10.1101/… on human germline mutation.
Shane McCarthy retweeted
Excited to announce our new review: Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References. w/ @BenedictPaten @rajivmccoy @khmiga @EimearEKenny et al. annualreviews.org/content/jo…
Shane McCarthy retweeted
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.
🧵
Shane McCarthy retweeted
In this preprint, Aylwyn Scally, Richard Durbin and I present evidence for deep population structure shared by all modern humans biorxiv.org/content/10.1101/… @aylwyn_scally @richard_durbin
Shane McCarthy retweeted
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/10.1101/…
Shane McCarthy retweeted
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.
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
Shane McCarthy retweeted
Delighted that our work on chromosome evolution in Lepidoptera is published today! ✨🦋
📰 Read ‘Comparative genomics reveals the dynamics of chromosome evolution in Lepidoptera’ with @sangerinstitute @SangerToL @darwintreelife @blaxterlab @CharJWright @marakat @phylewgenetics @EdinburghUni @thymelicus in @NatureEcoEvo ⤵️
nature.com/articles/s41559-0…
Shane McCarthy retweeted
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
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.
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.
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-ad).
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-c…). Come join us!
Shane McCarthy retweeted
The complete sequence of a human Y chromosome biorxiv.org/cgi/content/shor… #biorxiv_genomic
Shane McCarthy retweeted
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
Shane McCarthy retweeted
we are delighted to see the first of many @WellcomeOpenRes genome notes for Anopheles now out. this first one is a single insect @PacBio HiFi assembly for the major malaria vector Anopheles funestus. wellcomeopenresearch.org/art… 1/n
Shane McCarthy retweeted
Read our #DarwinTreeOfLife article for @NatureEcoEvo, where we ask "Does #genome size matter?"
For our scientists, trying to work out resources needed for each species, the answer is a resounding "yes!"
Find out more: ow.ly/9frb50Luabw
@KewScience @CibeleCaio @mcshane
Shane McCarthy retweeted
Safely sharing non-identifiable sequences from private cohorts of complete genome assemblies: privvg.github.io/2022/09/24/… (Or: How to build a global pangenome from siloed data)
Last day to apply for these roles with the @SangerToL Assembly Team!
We are recruiting for the Tree of Life Assembly team here @sangertol. With >500 genomes down, we are on our way to the @darwintreeoflife goal of generating high quality chromosomal assemblies for all eukaryotic species in the UK, but there are many challenges remaining.
Shane McCarthy retweeted
Not yet tired of pandemics? Why not read about the one caused by Wolbachia, an intracellular alphaproteobacterium, that's affecting insects and nematodes.
Read it here: biorxiv.org/content/10.1101/…
