GATK Dev Team (@gatk_dev) profile picture

GATK Dev Team

@gatk_dev

We are the computational biologists and software engineers who develop and support the Broad Institute's Genome Analysis Toolkit, or GATK.

 Cambridge, MA
broadinstitute.org/gatk
Joined June 2012
  • Tweets1.9K
  • Following54
  • Followers3.3K
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Photo by GATK Dev Team (@gatk_dev)Photo by GATK Dev Team (@gatk_dev)Photo by GATK Dev Team (@gatk_dev)Photo by GATK Dev Team (@gatk_dev)Photo by GATK Dev Team (@gatk_dev)Photo by GATK Dev Team (@gatk_dev)Photo by GATK Dev Team (@gatk_dev)Photo by GATK Dev Team (@gatk_dev)Photo by GATK Dev Team (@gatk_dev)Photo by GATK Dev Team (@gatk_dev)
Using a deep generative model, CellBender models and denoises droplet-based single-cell data and improves multiple downstream analyses. @broadinstitute @patrick_ellinor @gatk_dev nature.com/articles/s41592-0…

Unsupervised removal of systematic background noise from droplet-based single-cell experiments...

Nature Methods - Using a deep generative model, CellBender models and denoises droplet-based single-cell data and improves multiple downstream analyses.

nature.com
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Pretending to be a biologist this week - am learning so much in the @BioInfoCambs / @broadinstitute course on using the @gatk_dev for variant discovery 🧬
Image from Sarah Sandler (@sarahesandler)
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GATK Dev Team retweeted
Eric Dawson (@erictdawson) profile picture
Eric Dawson@erictdawson14 Dec 2022
Parabricks 4.0 is FREE for R&D, and the team made prebuilt workflows in #wdl and #nextflow available: developer.nvidia.com/blog/de… . They're on @TerraBioApp (terra.bio/nvidias-clara-para…), up to 24X faster, up to 2X cheaper, and publicly available on GitHub: github.com/clara-parabricks-…
Democratizing and Accelerating Genome Sequencing Analysis with NVIDIA Clara Parabricks v4.0 |...

Democratizing and Accelerating Genome Sequencing Analysis with NVIDIA Clara Parabricks v4.0 |...

Learn about NVIDIA Clara Parabricks v4.0, which brings significant improvements to how genomic researchers and bioinformaticians deploy and scale genome sequencing analysis pipelines.

developer.nvidia.com
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GATK Dev Team retweeted
Eric Dawson (@erictdawson) profile picture
Eric Dawson@erictdawson14 Dec 2022
Nvidia Clara Parabricks has accelerated #bwa, #gatk HaplotypeCaller, mutect2, DeepVariant, bam -> fastq, QC tools, functionally equivalent to community versions, up to _80X_ faster, FREE for R&D, + available with @nvidia AI Enterprise support: nvidia.com/en-us/clara/genom…
NVIDIA AI Platforms for Healthcare and Life Sciences

NVIDIA AI Platforms for Healthcare and Life Sciences

Explore open-source tools, APIs, frameworks, and GPU-accelerated pipelines designed for developers building solutions in drug discovery, medical imaging, genomics, healthcare robotics, and digital...

nvidia.com
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GATK Dev Team retweeted
GATK Dev Team (@gatk_dev) profile picture
GATK Dev Team@gatk_dev18 Oct 2022
Don't miss our interactive online workshop on DRAGEN-GATK this Friday, 10:30AM–12:30PM EST — Register today! gatk.broadinstitute.org/hc/e…

🗓️ DRAGEN-GATK Webinar [Oct. 21, 2022]

This October 21, join us for an interactive online workshop on Whole-Genome Analysis with DRAGEN-GATK! In this webinar, you will get the opportunity to will learn what it is, why it exists, and how...

gatk.broadinstitute.org
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GATK Dev Team retweeted
Terra (@TerraBioApp) profile picture
Terra@TerraBioApp13 Oct 2022
📣 Don't miss these interactive online #bioinformatics workshops — smash that register button today! terra.bio/get-trained-on-ter…
Get trained on Terra with our interactive online workshops - Terra

Get trained on Terra with our interactive online workshops - Terra

In response to popular demand, our User Education team has been running weekly interactive workshops to help newcomers get started with Terra. They’ve also developed some satellite workshops that use...

terra.bio
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GATK Dev Team retweeted
Alix (@alixcruse) profile picture
Alix@alixcruse31 Aug 2022
Read Terra's blog on the collaboration to adapt @UltimaGenomics data for GATK variant calling, which includes workspace preloaded with sample data and the fully configured analysis workflow: terra.bio/updated-gatk-pipel…
Try out the updated GATK pipeline for Ultima Genomics data - Terra

Try out the updated GATK pipeline for Ultima Genomics data - Terra

Computational biologist and GATK team member Megan Shand describes the new GATK pipeline for processing short-read WGS data produced by the Ultima Genomics technology.

terra.bio
Genome in a Bottle (@GenomeInABottle) profile pictureGenome in a Bottle@GenomeInABottle31 Aug 2022
Replying to @seankenneths
It appears that @UltimaGenomics WGS datasets for @GenomeInABottle samples are now available at ultimagenomics.com/blog/refe…
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Replying to @samuel_marsh @mikhaeldito313 @tangming2005 @DrYaraSanchez @gali_bai @constantAmateur
For those interested: New Terra Blog post on CellBender terra.bio/harness-machine-le…

Harness machine learning to clean up your scRNA-seq data - Terra

Guest author Stephen Fleming introduces CellBender, a software package for eliminating technical artifacts from high-throughput scRNA-seq and other multi-omics data.

terra.bio
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Human geneticist know its been a nightmare to call reliable #CNVs from #exome. Fortunately @TalkowskiLab helps calling CNVs on our @broadinstitute-sequenced samples. Image our excitement with the new benchmarked algorithm #GATK-gCNV biorxiv.org/cgi/content/shor… #bioRxiv! Awesome!
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1/Now available as advance online publication in _Bioinformatics_: "Assessing and assuring interoperability of a genomics file format", by @NiuJeffrey, @notabmovieactor, @DanielleDenisko, and me. academic.oup.com/bioinformat…
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GATK Dev Team retweeted
BOSC (@OBF_BOSC) profile picture
BOSC@OBF_BOSC5 Apr 2022
Our first #BOSC2022 gold sponsor is the Data Sciences Platform of @broadinstitute, broad.io/dsp, home of @gatk_dev and @terrabioapp! 🙌
Image from BOSC (@OBF_BOSC)
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GATK Dev Team retweeted
Terra (@TerraBioApp) profile picture
Terra@TerraBioApp25 Feb 2022
Replying to @TerraBioApp @googlecloud
Terra users can now specify the region of workspace buckets as well as storage and compute resources for Cloud Environments and #bioinformatics workflows.
Image from Terra (@TerraBioApp)
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4/12 We start with: - 63,237 exomes (>20,000 ASD) - SNVs/indels processed by GATK - Rare copy number variant (CNV) discovery by new tool GATK-gCNV - Genic constraint (LOEUF) from @gnomad_project - De novo, rare inherited, and case/control variants
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GATK Dev Team retweeted
Jack Kosmicki (@jakphd) profile picture
Jack Kosmicki@jakphd23 Dec 2021
CNVs are an area effectively ignored in the @uk_biobank exome papers and perhaps should be re-examined with this new GATK-gCNV caller (although I'm sure @TalkowskiLab, @RyanLCollins13 have probably already started exploring this in the UKB exomes😉).
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GATK Dev Team retweeted
Jack Kosmicki (@jakphd) profile picture
Jack Kosmicki@jakphd23 Dec 2021
Everyone knows CNV calling is tough in exome-seq data, so Fig. 1D is pretty impressive showing that @gatk_dev's GATK-gCNV caller performs shockingly similar between WES and WGS data.
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Initial alpha release of open-source DRAGMAP from @gatk_dev and the #DRAGEN team at @illumina - Introducing DRAGMAP, the new genome mapper in DRAGEN-GATK gatk.broadinstitute.org/hc/e…
Introducing DRAGMAP, the new genome mapper in DRAGEN-GATK

Introducing DRAGMAP, the new genome mapper in DRAGEN-GATK

As you may know from previous posts, we’ve been working with the DRAGEN team at Illumina to produce a new version of our Best Practices pipeline for germline short variant calling, called DRAGEN-GA...

gatk.broadinstitute.org
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GATK Dev Team retweeted
Hail (@hailgenetics) profile picture
Hail@hailgenetics10 Sep 2021
Hail v0.2.75 is out now! Bug fixes, performance improvements, and a new feature. Update your version when you can :) #hailGenetics #geneticsMadeEasy #scalableGenomics
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GATK Dev Team retweeted
Terra (@TerraBioApp) profile picture
Terra@TerraBioApp4 Aug 2021
New release brings GPU support to Jupyter Notebooks in Terra, accelerating ML analyses terra.bio/speed-up-your-mach…
Speed up your machine learning work with GPUs - Terra

Speed up your machine learning work with GPUs  - Terra

Terra has offered the ability to use GPUs in workflows for quite some time, yet many of you have told us that you also need to be able to run GPU-enabled computations interactively, so we're really...

terra.bio
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GATK Dev Team retweeted
Terra (@TerraBioApp) profile picture
Terra@TerraBioApp8 Jul 2021
New 2min video explains why #LifeSciences research is moving to the cloud and how Terra helps you focus on your science youtube.com/watch?v=w9mGcvU6… #Bioinformatics #CloudComputing
Terra in a nutshell

Terra in a nutshell

Terra is a scalable cloud platform for biomedical researchers to ac...

youtube.com
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GATK Dev Team retweeted
Terra (@TerraBioApp) profile picture
Terra@TerraBioApp6 May 2021
"GATK for Microbes" is also available as a preconfigured workspace in Terra app.terra.bio/#workspaces/he…
GATK Dev Team (@gatk_dev) profile pictureGATK Dev Team@gatk_dev5 May 2021
Catch up on the exciting « GATK for Microbes » developments presented by @bhanu_gandham, now available on YouTube!
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