Top Tweets for #GraphGenomes
Fantastic talk by @JGDPrendergast from @roslininstitute looking at #graphgenomes and conservation of #variants across mammalian species at the @ICBG2022 Symposium! #bovine #functional #genome
“… adds 119 million base pairs of euchromatic polymorphic sequence … relative to the existing reference”
This is going to be a game changer. Time to start using #graphgenomes
A Draft Human Pangenome Reference https://t.co/iEAlZYrToG #bioRxiv
28/ I want to congratulate my student @groza_cristian who is the graph magician in the lab. Can't wait to see where the next project will take us. Go #graphGenomes!
End of 🧵
1/ We've just finished 3 papers on #transposons #infection #epigenomics #graphGenomes, the result of an amazing collaboration with @LB_Barreiro and Tomi Pastinen. Start of a long 🧵
Stay tuned, if you like #transposons #epigenetics #infection and #graphGenomes. This week i will post about not just 1, not 2 but 3 papers that we're about to submit!
#graphgenomes have really helped us to simplify things conceptually and methodologically: Sampling kmers from the population, representing and analysing haplotype paths and allele frequencies, mapping kmers from reads etc. Much easier than the traditional linear model+vcf. 4/5
@infoecho @lh3lh3 For example https://t.co/qXjD4wbsX5 (hobby) is a #rdf4j using #sparql implementation against custom #GraphGenomes file formats. This allows compresed DNA data while accurately linking to annotations of what that DNA "does".
Pan-Genome of Wild and Cultivated Soybeans https://t.co/vQeN9bHBhe
> #Genomics #Bioinformatics #Bioinformatica #Pangenome #GraphGenomes
Enjoying cutting edge #java with project panama and #rust to get access to bleeding edge #GraphGenomes. Now let's wrap it into a #sparql endpoint #BioHackEU20 !
@EPOorg Shout out to @erikgarrison for making the wonderful #odgi #GraphGenomes and team #VG to base my #hobby work on with #python #rdflib. Reducing the gaps between the #protein and #dna DBs.
Presenting my poster on cancer-relevant variants (including #structuralvariation) in variation #graphgenomes at #ASHG19 this afternoon - come see me at 1011/W at 2pm! PDF is here: https://t.co/jlLNIwNuay
@JosiahSeaman @IPKGatersleben @UweScholz271 Nice talk! I am not really working with #genomes but I liked your concepts of visualisation, makes it indeed a lot more understandable. As @JJSzymanski mentioned it would be exciting to apply some #graphtheory and typically related measures to your #graphgenomes.
Today at @IPKGatersleben: Waterman Seminar with @JosiahSeaman from @kewgardens on ”FluentDNA Visualization: Scalable Graphics form Nucleotides to Populations”. #GraphGenomes #GenomeBrowser
A #GraphGenomes tubemap visualization which gets subgraphs to render using #SPARQL queries. Using a standard database as a #rest backend for convoluted DNA ;) Visualization and datamodel done by #vgteam (for the curious it basically re-implements vg chunk in 4 queries).
It will happen eventually! Bacteria already have a much more lenient definition of species when it comes to their genome content #graphgenomes #pangenomes
What are #GraphGenomes and how do they compare to #NGS #Mapping to the linear-based representation of the #HumanGenome ? See here the highlights of recent preprints on the subject: https://t.co/H2gNJo0ZBh #TheOmicsCast https://t.co/BklnyctDdn
After 40 hours back to the airport. Still looking forward to Pangenomics #NCBIhackathon @ucscgenomics followed by @GenomeInABottle workshop. Going to be an intense week with lots of discussions + some new insights into #graphgenomes, #SVs. @BCM_HGSC @MedhatHelmy7 @DCGenomics
It’s out! Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes #graphgenomes @IvarGrytten @kuppern87 @SandveGeir https://t.co/1YgkpBd5Ay
Come find me at poster 1511 2-4 @ #ASHG18! I’ll be presenting a small toolkit for working with #graphgenomes in GFA format. Always happy to talk sv calling, mutational sigs, genome assembly, etc!
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