New short paper from Joel Hellewell and Sam Horsfield and on making pangenome (specifically frequency estimates) from metagenome data:
biorxiv.org/cgi/content/sh…

🧬🔍Very interesting to see how recently active #TransposableElements can be read out from pangenome graphs. Seems like a very good way forward to identify active TEs.

by pio Richard Durbin

doi.org/10.1101/2024.0…

Pantera: Identification of transposable element families from pangenome polymorphisms biorxiv.org/content/10.110…

Final session at #HGM2024 kicks off with Karen Miga explaining why we need a human pangenome as a true reference genome. Not least so we can investigate the important regions & populations we have largely ignored in the last 20 years.

It's going to be disruptive. 🙂

Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data. #Pangenomes #HostRemoval #Metagenomics GigaScience
academic.oup.com/gigascience/ar…

Human Pangenome Reference Consortium-

The Human Pangenome Reference Consortium (HPRC) is a project funded by the National Human Genome Research Institute to sequence and assemble genomes from individuals from diverse populations in order to better represent genomic landscape of…

Pantera: Identification of transposable element families from pangenome polymorphisms biorxiv.org/content/10.110…

Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome pnas.org/doi/abs/10.107… PNASNews

pnas.org/doi/10.1073/pn…

VRPG: an interactive visualization framework for reference-projected pangenome graph
biorxiv.org/content/10.110…

Sam has then wrapped it all up in a nice snakemake pipeline CELEBRIMBOR (Core ELEment Bias Removal In Metagenome Binned ORthologs) which lets you go from MAGs to pangenome
github.com/bacpop/CELEBRI…

Regardless, we can generate a primary assembly and sidestep the issues of haplotype phasing, producing a highly contiguous (contig N50 91 Mb) and complete (99.7% of conserved mammalia genes) genome. We can then build a bovine pangenome with other bison/yak/bos. 2/3

Opinion piece by Jo Wolfe on our recent paper on pangenome evolution. sciencedirect.com/science/articl…

Our paper is here: pnas.org/doi/abs/10.107…

Identification of transposable element families from pangenome polymorphisms biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

#genomeassembly #triobinning #pangenome #wisent #longreadsequencing #endangeredspecies

Human pangenome reference consortium. Will
Need new data structure (a pangenome graph).
And it has to be open access.
All mapping of transcriptome etc will have to migrate on pangenomes.
Some key words:

ELSI …
Automated T2T assemblies
60x coverage
Phases up to 550 genomes

pantera receives as input a list of gfa files of non overlapping variation graphs and produces a library of transposable elements found to be polymorphic on that pangenome.

Identification of transposable element families from pangenome polymorphisms. #TransposableElements #TEs #Pangenomes #Polymorphisms bioRxiv
biorxiv.org/content/10.110…

Identification of transposable element families from pangenome polymorphisms
biorxiv.org/content/10.110…

EVG (Ensemble Variant Graph-based tool) can accurately genotype SNPs, indels, and SVs using short reads. EVG achieves higher genotyping accuracy and recall with only 5× sequencing data. EVG remains robust even as the number of nodes in the pangenome graph increases.