New review article in The Lancet Microbe

Economic evaluations of whole-genome sequencing for pathogen identification in public health surveillance and health-care-associated infections: a systematic review

https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(23)00180-5/fulltext

#WGS #PublicHealth #HAI #InfectiousDiseases #IDMastodon #Microbiology

''he non-negative sample was forwarded to NVSL, where it was identified as #HPAI #H5N6 from #WGS. The virus is a #reassortant of genotype B1.3 with a North American N6 gene. ''

The Armed Forces of #Ukraine switch to the WGS-84 world coordinate system, commonly used by #NATO countries, instead of the Soviet SK-42, which is accurate only for the territory of the former #USSR.
Establishing #coordinatesystems of the Alliance will improve the compatibility of troops and ensure the exchange of data between the Ukrainian army and other states. With the transition to #WGS-84 maps will become more accurate since SK-42 was based on a different mathematical model of the #Earth.

#Population-based #SARS-CoV-2 #WGS and contact #tracing during the #COVID19 pandemic in #Switzerland https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiad074/7086594?rss=1

Learning about MetaSTAAR, a package for meta-analysing whole genome sequencing studies. Common variant genotype meta-analysis would just operate on the level of aggregation of slices through the variants × studies array.

https://github.com/xihaoli/MetaSTAAR #GWAS #WGS

RT @micheome@twitter.com

I know I asked before, but can't locate the thread, where are you uploading WGS microbiome data from human samples? We've pulled off the human reads, but SRA is a pain & wondering if there is an easier way?

Please help 🙏 #microbiome #wgs #data #openscience

🐦🔗: https://twitter.com/micheome/status/1613280550189694977

RT @AntoBeck@twitter.com

Important #multiomics study from @SickKidsnews@twitter.com in Canada. #WGS #WTS and large panel #sequencing to profile childhood #cancer, helping to improve understanding, diagnoses and treatment. #genomics #genetics #transcriptome #fusions @sickkids@twitter.com https://go.nature.com/3Gz4vgH

🐦🔗: https://twitter.com/AntoBeck/status/1609688440727117827

''According to the study, 30 #Omicron strains that have been identified globally were measured in more than 300 randomly selected viral #WGS from #patients in #Shanghai, including mainly #BF7, #BA52, and the recently emerged #BQ1 and #XBB.'', https://journal.hep.com.cn/fmd/EN/10.1007/s11684-022-0981-7

''Since the beginning of December, the #China CDC has completed the #WGS of 1,142 cases through a sampling survey and found that the #Omicron subvariants #BA52 and #BF7 were the dominant strains, accounting for more than 80 percent of the total, said Xu. There are also seven other subvariants of Omicron circulating.'', GT: https://www.globaltimes.cn/page/202212/1282775.shtml

https://www.nature.com/articles/s41588-022-01225-6 "Powerful, scalable and resource-efficient meta-analysis of #rareVariant associations in large whole genome sequencing studies" #wgs #genetics #genomics #bioinformatics #MetaSTAAR performs rare variant meta-analysis at scale and produces results comparable to using pooled data. We further demonstrate that MetaSTAAR is scalable to biobank-scale cohorts through meta-analysis of #TOPMed WGS data and #UKBiobank WES data of ~200,000 samples.

RT @jsantoyo@twitter.com

Imputation of low-coverage sequencing data from 150,119 UK Biobank genomes. #UKbiobank #GenotypeInputation #WGS @biorxivpreprint@twitter.com
https://www.biorxiv.org/content/10.1101/2022.11.28.518213v1

🐦🔗: https://twitter.com/jsantoyo/status/1605331678779637763

Low coverage WGS + UKB imputation reference panel (based on 150k whole genomes) is a great combo.

RT @jsantoyo@twitter.com

Imputation of low-coverage sequencing data from 150,119 UK Biobank genomes. #UKbiobank #GenotypeInputation #WGS @biorxivpreprint@twitter.com
https://www.biorxiv.org/content/10.1101/2022.11.28.518213v1

🐦🔗: https://twitter.com/jsantoyo/status/1605331678779637763

Our paper, with Dr Wei and @gustavo_silva about genomics of colonization stressful habitats around the Atacama in a wild tomato species is out in @NewPhytologist. Interestingly, our results support that colonization to new stressful habitats is mediated by the emergence of adaptive variation in numerous core elements of gene networks related, for example, to flowering time. https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.18634.
#adaptation #climatechange #popgen #genetics #WGS #evolution #wildtomato #Solanaceae #openaccess

Sebastian with his favorite frisbee
#dogsofmastodon #WGS

Sebastian with his favorite frisbee
#dogsofmastodon #WGS

https://www.nature.com/articles/s41598-022-26181-3 "Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment" #gatk #dragen #deepvariant #genomics #wgs

A lot of software can provide genotype likelihood for a #WGS #NGS sample, only one I know provide the likelihood of ALL 10 genotypes for a site, i.e. ANGSD.

Anyone knows any software that calculate all allele likelihood for a site? So I wanna know the probability of observing allele A, C, G, and T in a site. The ones I found only provide probability of one allele (consensus/random).

#Genomics #genomic #PopulationGenomics #bioinformatic #compBio

:boost_ok: :boost_requested: :mastoread:

A lot of software can provide genotype likelihood for a #WGS #NGS sample, only one I know provide the likelihood of ALL 10 genotypes for a site, i.e. ANGSD.

Anyone knows any software that calculate all allele likelihood for a site? So I wanna know the probability of observing allele A, C, G, and T in a site. The ones I found only provide probability of one allele (consensus/random).

#Genomics #genomic #PopulationGenomics #bioinformatic #compBio

Great meeting at the New York Genome Center tonight @nygenome@twitter.
Marcin Imielinski, Dan Landau, Nico Robine presenting the future of #WholeGenomeSequencing cancer.

#WGS #cancer
Do you use #WGS?

Is it too soon for Tech & Biotech companies to make a jump from Twitter to Mastodon? Do you want to follow along with #InfectiousDiseaseDiagnostics #MachineLearning #WGS innovations in #HAI and #AntibioticRestistance control? #DZD