WUR_AppliedBioinfo @appliedbioinfo

Joined January 2019

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CSHL Meetings @cshlmeetings

3 years ago

#BoG22 kicked off last night! This is the first one in person since 2019 and it is great to have this community back on campus. For more info on this annual meeting: bit.ly/BoG22

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WUR_AppliedBioinfo @appliedbioinfo

6 years ago

Also worked great for plants... @10xGenomics any alternative for genomes?

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Gencove @Gencove

6 years ago

We'll be at the BGI workshop 2.30pm discussing low-pass sequencing as a replacement of genotyping arrays across species. We are also at booth #624 till 3pm. Come see us! #PAGXXVIII

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carla silva 🌱🔬💻🇧🇷☕🎶🔭 @silvacbio

6 years ago

Congrats @jvhaarst, @LindaVeronique, @appliedbioinfo

Sol Genomics Network @solgenomics

6 years ago

Congrats @jvhaarst, @LindaVeronique, @appliedbioinfo

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Jason Chin @infoecho

6 years ago

I like the conclusion part 😆... seriously, all assemblers have pros and cons. The design goal and implementation details matters. #PAG2020

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Rick Masonbrink @remkv6_rick

6 years ago

Zachary Lippman, “Aroma, size, and productivity in tomato are due to structural variants.” 40% of SV within and nearby genes with 80% in regulatory regions. #PAG2020

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Circulomics @circulomics

6 years ago

Nice results from @GiessenSingh sequencing canola on @nanopore using SRE XL. #PAG2020 #PAGXXVIII

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@bioinfo_mark @sergekoren @ArangRhie Depends on the genome. HiFi good at resolving segmental duplications, so long as there are variants every few kbp, and achieves high continuity and quality (Q50+). For more recent dups and large tandem arrays (e.g. centromeres), ultra-long is needed

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Liz Tseng @Magdoll

6 years ago

Kerelska: Falcon-Unzip now accepts HiFi (aka CCS) input whiich results in reduced runtime and better assembly. #SMRTInformatics @PacBio

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Liz Tseng @Magdoll

6 years ago

.@acarroll_ATG: single DeepVariant production mode (v0.8) for @PacBio HiFi, can accept mixed (1M or 8M), runs 30X genome in 5 hours 320 CPU hours github.com/google/deepvar…

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Jason Chin @infoecho

6 years ago

Jay from @DTGenomics combines Peregrine and Omni-C technology for end-to-end chromosome level haplotype resolves assembly. #PAG2020 #PAGXVIII

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Kevin McKernan @Kevin_McKernan

6 years ago

Phased Cannabinoid Synthase gene cluster. HiFi chemistry with Peregrine assembler. Genome assembled in 70mins. We’ve been trying to sort this out since 2011. @infoecho @PacBio

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Sergey Koren @sergekoren

6 years ago

My presentation from #PAG2020 #PAGXXVIII this morning on HiCanu assembly: speakerdeck.com/skoren/hicanu-…

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Adam Phillippy @aphillippy

6 years ago

Listen to @kerstin_howe for 10 minutes and you’ll never trust a genome assembly again. So ... many ... errors. Great work by her curation team at @sangerinstitute fixing @genomeark assemblies and guiding assembly method improvements #PAGXXVIII

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Rick Masonbrink @remkv6_rick

6 years ago

Raphael Mercier triggered male genome elimination to obtain clonal plants in up to ~30% of progeny using a combination of three mutations to turn meiosis into mitosis. Engineering a male-specifically expressed gene into females enabled haploid embryo development. #PAG2020

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Rick Masonbrink @remkv6_rick

6 years ago

Raphael Mercier increased recombination rates in Arabidopsis, pea, rice, and tomato from 3-8x using mutants, and found that the extra crossovers maintained the same distribution across chromosomes, with recombination repression still occurring in centromeres. #PAG2020

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Kelly Dawe @corncolors

6 years ago

Merging two independent assemblies (one from PacBio and another Nanopore), guided by Bionano maps, yielded a dramatically improved assembly of an inbred carrying maize Abnormal chromosome 10. The contig N50 is 162 Mb, with two fully gapless chromosomes. biorxiv.org/content/10.110…

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IGV Team @igvteam

6 years ago

IGV 2.8 released. Many new features and improvements. See the release notes at software.broadinstitute.org/software/igv/2…. #genomics #NGS #bioinformatics

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Genome Biology @GenomeBiology

6 years ago

Wang and Au benchmark hybrid error correction methods for nanopore and PacBio long read data. They compare alignment-based and de Bruijn graph-based approaches. If the error rate is below 19%, perfect correction is possible genomebiology.biomedcentral.com/articles/10.11…