Henri van de Geest

@geesthc

Bioinformatician @ Genetwister The Netherlands

Wageningen
Vrijeme pridruživanja: kolovoz 2009.

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  1. 4. velj
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  2. proslijedio/la je Tweet
    3. velj

    Introducing "Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED" with et al. Does selective enrichment and depletion of any targeted genomic region purely in software for sequencing.

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  3. 31. sij

    Check if you want to see my colleague Bart Nijland talking about our tetraploid Rose assembly with pacbio HiFi reads.

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  4. proslijedio/la je Tweet
    27. sij
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  5. proslijedio/la je Tweet
    16. lis 2019.

    V2.0 of the MIBiG database of known biosynthetic gene clusters is now online! 851 BGCs have been added since version 1.0, and annotation quality improvements for another ~600. Website: The NAR update paper is available here:

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  6. 24. sij

    Can watch this whole day ;-)

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  7. 24. sij

    Single 8M chip ccs takes ~5hrs on a single AMD Epyc 7742 128 core server. It takes ~18hrs on our ~3 year old Intel Xeon Broadwell 56 core E7-4830v4. That's fast and a nice improvement over 'old' hardware! (until ccs is performed onboard sequel2...)

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  8. 17. sij

    great work! These high accurate reads bring new possibilities seeing how many 'new' assemblers have shown up lately.

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  9. 16. sij

    Thanks! Do you think these optimizations also apply for ONT data? Like hpc and systematic error detection?

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    15. sij

    . : Nighthawk phases bubbles, fast and accurate

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  11. 15. sij

    Thats impressive... Personally I really like the assembly times. With erroneous reads this would take ages. Imagine assemble 500gb of raw data, thats not cheap

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  12. 14. sij

    A game changer it is, shorter reads, but better assemblies.

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    14. sij

    If you are not in , or can't attend the session, here is my slide deck on Peregrine Assembler and Cannabis genome assembly results: If you have any questions, let me know.

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    14. sij

    Zach Lippman: long-read sequencing on PromethION revealed 240k SVs across 100 tomato genomes

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  15. 14. sij
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    13. sij

    MV: Showing system/sequencing improvements: -1 human HiFi genome/SMRT Cell - reduce movie times - improved CCS analysis speed/accuracy - HiFi directly off instrument

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    13. sij

    CCS generation coming to the instrument in 2020. Error free reads coming off the Sequel II.

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  18. 14. sij

    "With..reads (>150 kb), we see that SV recall decreases ... we hypothesize this reduction in performance is an analytic limitation and not due to the increased fragment length itself" seems same behavior with very distinct alleles, many SV's within 1 read.

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  19. 14. sij

    the latest CANU git pull with Homopolymer compression did a great job on HiFi!

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  20. proslijedio/la je Tweet
    13. sij

    up next tetraplid rose assemblies by Bart Nijland from

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