Read on Twitter
The VGP announces a special @nature issue w/flagship & other genome assembly pubs focused on quality, standardization & scale @RockefellerUniv @HHMINEWS @genomewarriors @sangerinstitute @maxplanckpress @genome_gov @MT_Genetics @Genome10K #VGPFlagship https://bit.ly/3vo6Ja4
With these pubs, we introduce a new era of quality in comparative genomics. This thread highlights some of the state-of-the-art & numerous tech improvements. You can also read every @nature article from the special issue. https://go.nature.com/2Pn4WTk
The flagship describes the feasibility for achieving specific minimum quality metrics w/novel algorithms that pieces the genome assembly puzzle together
@ArangRhie @mcshane @ofedrigo @kerstin_howe @TheGeneMyers @richard_durbin @aphillippy @erichjarvis https://go.nature.com/3sZznNn
@ArangRhie @mcshane @ofedrigo @kerstin_howe @TheGeneMyers @richard_durbin @aphillippy @erichjarvis https://go.nature.com/3sZznNn
Our VGP assembly pipeline uses a combo of long-read sequencing, linked-read sequencing, optical mapping & Hi-C data in an auto workflow w/manual curation, significantly reduces the number of assembly errors
@kerstin_howe https://bit.ly/3xwVIFx
@kerstin_howe https://bit.ly/3xwVIFx
We also assembled complete vertebrate mitogenomes, which revealed widespread gene duplications and repeats @giulio_formenti @MahUliano @jenbalacco @sergekoren
https://bit.ly/2QZQsZT
https://bit.ly/2QZQsZT
Many errors are mostly due to algorithms not properly separating homologous haplotypes of maternal & paternal chromosomes. One solution is a trio binning approach.
@sergekoren @arangrhie @aphillippy https://bit.ly/32NysVu
@sergekoren @arangrhie @aphillippy https://bit.ly/32NysVu
For cases where parental data is unavailable, another solution is an algorithm we developed called FALCON-Phase that reduces the computational complexity of separating these sequences at chromosome scale
@zevkronenberg @drsarahdoom @ivanliachko
https://bit.ly/3evCrvf
@zevkronenberg @drsarahdoom @ivanliachko
https://bit.ly/3evCrvf
To date, the VGP pipelines have led to the submission of 129 diploid assemblies representing the most complete and accurate versions of those species to date
https://bit.ly/32OmkDD
https://bit.ly/32OmkDD
All VGP genomes, annotations & alignments are publicly available. Find them in international public genome browsing & analyses databases @NCBI @ensembl @genomebrowser @dnanexus
https://bit.ly/3xyPDbA
https://bit.ly/3xyPDbA
Our VGP pipelines are also open source & publicly here https://vertebrategenomesproject.org/technology
It takes a village! Many other consortia, projects & institutions collaborated on the flagship & other papers @SangerToL @darwintreelife @bat1kgenomes @B10K_Project @HumanPangenome @EBPgenome @northeastern @sandiegozoo @NUMarSci
A massive shout out to our technology partners @PacBio @nanopore @illumina @ArimaGenomics @PhaseGenomics @DTGenomics
