#pangenome — Public Fediverse posts

@foaylward
PanGraph was recently rewritten into #Rust to further speed up wall clock time:
https://github.com/neherlab/pangraph

Both Panalyze and PanGraph can export the graph to GFA format, which then conveniently allows the use of the vg toolkit (vg deconstruct, vg call) to extract variants into vcf format.

There are other #pangenome graph methods and also the de bruin-based approaches, but this reply is already too long! Let me know how your variant discovery develops. Hope this helps a little bit.

@foaylward
Github: https://github.com/downingtim/Panalyze/

#PanGraph could be another #pangenome graph option if you find pggb to be too compute intensive. PanGraph uses a progressive MSA strategy based upon a guide tree so it scales ~linearly to the # of input genomes (unlike pggb-based programs that are quadratic w.r.t. the # input genomes due to its all-vs-all pairwise alignments). PanGraph should be faster but sacrifices some global optimality due to its guide tree use.

Cochetel & Cantu publish a new MBE Review on plant pangenomes, outlining major paradigms from gene-based catalogs to haplotype-resolved graphs, core and variable compartments, and how graph-based frameworks enable analyses that are difficult with single linear references.

🔗 https://doi.org/10.1093/molbev/msag087

#evobio #molbio #pangenome

Abbot et al. present a pangenome analysis of the endofungal genus Mycetohabitans, showing bacteria-fungus coevolution.

🔗 https://doi.org/10.1093/gbe/evaf231

#genome #evolution #pangenome

Going through Samuel Horsfield's presentation on pangenome graphs in comparative genomics, courtesy of EMBL.

Fascinating tidbit on history of alignment based sequence graph - it goes all the way back to 1989 (Hein), era of Apple IIs and IBM PS/2s. Great talk!

#pangenome #microbiology #bioinformatics

Researchers decoded the #pangenome of 33 oat lines, revealing their full #geneticdiversity to support breeding of more resilient, high-yield #crops in the face of #climatechange: http://go.tum.de/651300

📷iStock/ Evgeniy Andreev

I got a shoutout during an EMBL lecture presentation on indexing pangenomes. I have to admit, it made my day 😄

The whole series is fantastic so far, the particular talk on indexing can be found below with slides and video:

https://www.ebi.ac.uk/training/events/making-sense-massive-genomic-data-indexing-scale/

#bioinformatics #pangenome #education

Minigraph to dotplot to image to AI-assited SV detection
Looks like worth trying
https://www.biorxiv.org/content/10.1101/2025.07.06.663386v1.full.pdf
https://github.com/songbowang125/Swave
#bioinformatics #Genomics #pangenome #ShouldTryThis

Heng Li: "If you want to check if a human gene has copy-number changes or lands in a complex region, try http://pangene.bioinweb.org. Recently updated with more and better assemblies."

https://xcancel.com/lh3lh3/status/1915934587601014926#m

#pangenome #bioinformatics

Pipeline release! nf-core/pangenome v1.1.3 - pangenome 1.1.3 - marsupial!

Please see the changelog: https://github.com/nf-core/pangenome/releases/tag/1.1.3

#pangenome #nfcore #openscience #nextflow #bioinformatics

🌱 Exciting Advances in Tomato Breeding with Project INNO-TOM 🍅
We're thrilled to share that Computomics is part of the consortium working on the groundbreaking INNO-TOM project, funded by Germany's BMBF. This initiative aims to develop innovative tomato varieties that are both disease-resistant and nutrient-enriched.

More 👉 https://www.computomics.com/news-reader/inno-tom.html

#Agritech #AI #Pangenome #SustainableAgriculture #Tomatoes #InnoTom

"Approaches to studying virus pangenome variation graphs" - https://arxiv.org/abs/2412.05096 new #genomics #pangenome preprinted review paper, currently in review. #virus #pathogen #graph

Very timely!!
#Pangenome construction from short-read sequences: benchmarking for population and conservation genomics

https://www.authorea.com/users/616600/articles/1242237-pangenome-construction-from-short-read-sequences-benchmarking-for-population-and-conservation-genomics

Exploring gene content with #pangenome gene graphs https://arxiv.org/abs/2402.16185 "We developed pangene, a computational tool to identify gene orientation, gene order and gene copy-number changes in a collection of genomes."

#ucsc #pangenome : "No single reference genome such as hg19 or hg38 can accurately represent human genetic diversity. The H#PRC's goal is to improve this by sequencing thousands of human genomes at high quality and building new tools to improve working with them. The first data release from this project consists of 47 phased, diploid assemblies, more than 99% accurate at the structural and base pair levels." https://genome.ucsc.edu/goldenPath/newsarch.html

"We propose that at least part of the #pangenome can be understood as a set of #genes with relationships that govern their likely cohabitants, analogous to an ecosystem’s set of interacting organisms. Our findings indicate that intragenomic gene fitness effects may be key drivers of #prokaryotic #evolution, influencing the repeated emergence of complex gene–gene relationships across the pangenome."

https://www.pnas.org/doi/10.1073/pnas.2304934120

"Revisiting pangenome openness with k-mers" - pangrowth

Looks very useful!

#pangenome

https://www.biorxiv.org/content/10.1101/2022.11.15.516472v3

Some really great talks and discussions today on advances in virus-livestock omics at the #Turing institute, who kindly supported the event. Talks include those by Ge Wu and Marie Di Placido (pictures) from the #Pirbright Institute.

Great to have input from the #BBSRC and #SFTC #Harttree Centre too.

Looking forward to new adventures in this area...

#livestock #virus #genomics #antibody #genome #mutation #pangenome #omics #transcriptomics #spatialtranscriptomics #fmdv​

Last chance to register for our meeting "Advancing virus-livestock omics" on Thurs 28th Sept at the Alan Turing Institute.

Registration closes end of Mon 25th.

See https://www.turing.ac.uk/events/advancing-virus-livestock-omics

Register here: https://t.ly/wYA7d

Schedule below

Zoom stream possible for those from further afield

#livestock #virus #genomics #antibody #genome #mutation #pangenome #omics #transcriptomics #spatialtranscriptomics #fmdv

Sweet. I mean, double-sweet. Watermelon genome studies find prior domestication doubled the sugar transporter.

Also found useful disease-resistant genes that might be useful to put back in to modern cultivars.

#CRISRP 🍉 , plz.
#scicomm #genomics #pangenome #PlantBreeding

https://btiscience.org/explore-bti/news/post/behind-the-rind-new-genomic-insights-into-watermelon-evolution-quality-and-resilience/

Heck of a lot more organized than the first #phage #pangenome test I threw together, but still very much iffy. I was hoping the new genes as nodes attempt would pay off, but I'm beginning to think high degree of nucleotide level variation and mosaicism in phages does not mix well with brute force pangenome attempts.

#Phage family #pangenome test. I really wasn't expecting much in the beginning, but the dataset is starting to look pretty interesting.

Been testing out half a dozen or so pangenome building pipelines/libraries. I'll definitely do a write up of the experience soon.

Another fun tool from Heng li - pangene for constructing pangenome graphs from assemblies.

https://github.com/lh3/pangene

Utilizing provided list of proteins (via miniprot) to construct graphs around it sounds interesting! #bioinformatics #pangenome