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Erik Garrison proslijedio/la je Tweet
Theory part of our work with Kristoffer Sahlin
@krsahlin out: https://arxiv.org/abs/2001.06864Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
Let's (almost losslessly) project pangenome graphs into BED and FASTA and then query them with bedtools! https://github.com/vgteam/odgi/pull/67 … cc
@aaronquinlan@lh3lh3@BenedictPaten@jeizengaHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
Erik Garrison proslijedio/la je Tweet
Fellowships available to cover travel expenses and child care for the fourth
#EMBOpopgen course http://meetings.embo.org/event/20-populationgenomics … thanks to@EMBOevents,@sibe_iseb, SIGA, AGI! Deadline for application *28 January 2020*@chiarabatini@DrManicapic.twitter.com/NRRylOgBgl
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Documenting the HandleGraph abstraction and python library for variation graphs in odgi https://github.com/vgteam/odgi/blob/master/docs/handlegraph.md …. Work with big genome graphs in little space.
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Is there any way to convert a cram to paired FASTQ in a streaming manner?
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Erik Garrison proslijedio/la je Tweet
The roadmap is all planned out: Efficient
#programming session during the week-long#hackathon for a#genomegraph hosted by@computomics#ggbhtu2k19@t_teogene@QBIC_tue@PlantEvolutionpic.twitter.com/NUxaEYvt6z
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Erik Garrison proslijedio/la je Tweet
Have wgs and want sensitive mitochondrial variant calls? If you're relying on what your nuclear variant caller gives you, you'd be surprised how much you're missing...https://twitter.com/biorxiv_bioinfo/status/1197987127918780416 …
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Erik Garrison proslijedio/la je Tweet
We're excited for the first
@GenomeInABottle benchmark for the MHC! See Justin Wagner's poster at#gi2019 by@infoecho@tobiasmarschal@MikkoRautiaine3@erikgarrison... A Diploid Assembly-based Benchmark for Variants in the Major Histocompatibility Complexhttps://www.biorxiv.org/content/10.1101/831792v1 …Prikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
gimbricate v0.1: correcting overlaps *and* converting the corrected GFA into FASTA and PAF for use in pangenome aggregationhttps://github.com/ekg/gimbricate
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Erik Garrison proslijedio/la je Tweet
Thanks a lot to all participants of our
#genomegraph survey! There is still some time left to take part. It only takes 3 minutes!@QBIC_tue and@computomics value each single feedback to develop a tool which suits your needs. https://buff.ly/2p9SWae#pangenomepic.twitter.com/DArEjErZbw
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this implements the full "handlegraph" API, supporting construction and destruction of graph nodes (handles), edges (pairs of handles), paths (path handles), and path steps (step handles), plus GFA `g = odgi.graph(); g.create_handle("GATTACA"); http://g.to _gfa()`
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A (draft) python module succinct variation graphs https://github.com/vgteam/odgi/pull/52 …. Builds in lib/, `import odgi; help(odgi)` for documentation. Seeking comment with the aim to extend this to all the models in https://github.com/vgteam/libbdsg .
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gimbricate: for when you really need your GFA overlaps to be correct,https://github.com/ekg/gimbricate
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Is there any way to "cut" a SAM/BAM file to a particular region, so that alignments and their sequences are trimmed and cigars are updated to match wherever they overlap the region ends?
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Erik Garrison proslijedio/la je Tweet
Removing reference bias in ancient DNA data analysis by mapping to a sequence variation graphhttps://www.biorxiv.org/content/10.1101/782755v1 …
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Erik Garrison proslijedio/la je Tweet
Exciting days ahead. The Pangenome Project is going to have tremendous impact on genomics. Setting goals for T2T and comprehensive variant discovery.
@ucscgenomics@BenedictPaten@AkesonUCSC@mitenjain@HOlsenUCSC@ed_green_72@erikgarrison@NHGRIhttps://news.ucsc.edu/2019/09/pangenome-project.html …Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
Is there a forward evolution simulator that generates realistic structural variation mutations alongside the usual small variants?
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We're starting a user forum for vg and variation graph related topics: https://www.biostars.org/t/vg/ . Many thanks to
@biostars for making it easy!Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
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#CPANG19: Learn to use the variation graph data model to solve informatic problems caused by genomic diversity! (https://docs.google.com/presentation/d/17kJDi0ANrViNayGJKcdBZxw-B8sp6VfcCF9_PBibrLI/edit?usp=drivesdk … outlines what we will cover) https://twitter.com/erikgarrison/status/1157954458711666689 …pic.twitter.com/qh7RP4Zcqr
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