Jean P. Elbers
@jpelbers.bsky.social
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📥 157
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Bioinformatician, Vienna, Austria
reposted by
Jean P. Elbers
Heng Li
1 day ago
Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at
arxiv.org/abs/2606.15357
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Jean P. Elbers
bioRxiv Bioinfo
1 day ago
DynamicDemiLog: A Single Sketch for Ultrafast Similarity, Frequency, and Cardinality Estimation
https://www.biorxiv.org/content/10.64898/2026.06.12.731986v1
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The US Navy is using
@nanoporetech.com
sequencers in the field.
www.wadsworth.org/news/wadswor...
and
defence--blog-com.cdn.ampproject.org/v/s/defence-...
#nanopore
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The Wadsworth Center Advises the U.S. Navy Core Genomics Laboratory on Forward-Deployed Pathogen-Agnostic Threat Detection | New York State Department of Health, Wadsworth Center
The Navy Force Health Protection Command (FHPC) is establishing a new Core Genomics Laboratory in Florida to enhance pathogen detection and genomic surveillance capabilities for forward-deployed milit...
https://www.wadsworth.org/news/wadsworth-center-advises-us-navy-core-genomics-laboratory-forward-deployed-pathogen-agnostic
1 day ago
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Jean P. Elbers
Rasmus Kirkegaard
9 days ago
Is
@nanoporetech.com
hac v6 better than 5.2.0 sup? The short answer is no. But are a few errors in a genome worth 5 times more basecalling compute?
github.com/Kirk3gaard/M...
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Jean P. Elbers
Jonathan Göke
9 days ago
Nanopore sequencing provides not just long reads, but the the raw signal data can also be used to identify RNA and DNA modifications. This repository (and the associated review) lists some of the great tools that have been developed
www.cell.com/trends/genet...
add a skeleton here at some point
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Jean P. Elbers
Jonathan Jacobs
12 days ago
Hey
#genomics
and
#bioinformatics
community: I need an "endorsement" in order to submit a preprint to
@arxiv.bsky.social
😭 I'm registered, but can't submit our preprint to q-bio\GN (Genomics) section until we get an endorsement from an existing arXiv author w/endorse privileges. that you? plz DM me🙏
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Jean P. Elbers
Mihail Zdravkov
15 days ago
I've been working an a small Julia library for working with raw nanopore sequencing signals. It's still under development and not very mature, but maybe someone may find it useful and want to experiment with it. It provides functionality for signal-to-sequence alignments, basic signal scaling […]
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Original post on mastodon.green
https://mastodon.green/@mzdravkov/116680216574625654
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Jean P. Elbers
Phoronix
17 days ago
NBD-VRAM Provides Swap Space On Your NVIDIA GeForce GPUs -
https://www.phoronix.com/news/NVIDIA-NBD-VRAM
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NBD-VRAM Provides Swap Space On Your NVIDIA GeForce GPUs
An open-source developer has created NBD-VRAM as a way to create swap space on your consumer NVIDIA GPU's video memory under Linux...
https://www.phoronix.com/news/NVIDIA-NBD-VRAM
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reposted by
Jean P. Elbers
Seth Stadick
16 days ago
github.com/sstadick/str...
Stay in the code. Avoid context switching. That was the whole goal of this endeavor. I wanted to be able to use agents for things like search, one-off questions, and small patches without stepping out as abstracted as something like claude.
github.com/sstadick/str...
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Jean P. Elbers
Karl Seguin
18 days ago
I updated Learning Zig to work with 0.16
www.openmymind.net/learning_zig/
#Ziglang
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Jean P. Elbers
Christine He
19 days ago
Come to ONT's industry event at ASM to hear about two exciting new tools from
@jimshaw.bsky.social
! SNPmers (polymorphic kmers) are leveraged for impressive performance in both myloasm (metagenomic assembly) and savont (16S ASVs). Registration link 👇
add a skeleton here at some point
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Jean P. Elbers
bioRxiv Bioinfo
19 days ago
Memory-safe high-performance sequence mapping with rammap
https://www.biorxiv.org/content/10.64898/2026.05.26.726289v1
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Jean P. Elbers
Sebastian S. Cocioba
20 days ago
SPLICECRAFT v1.0 IS LIVE!!!!!!!!!!!! Open your terminal and type in "pipx install splicecraft" if you want to try it out, then spam "splicecraft update" often as I push updates frequently. A labor of love for the community I adore. Enjoy! 💚
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Jean P. Elbers
Joachim Goedhart
27 days ago
Awesome idea, bridging Excel with ggplot2 ⬇️ Figra: A WebAssembly-based Excel Add-in for publication-quality scientific visualization with ggplot2 by Yoshiaki Sato:
www.biorxiv.org/content/10.6...
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https://www.biorxiv.org/content/10.64898/2026.05.06.723320v1?ct=ct
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Jean P. Elbers
James Ferguson
26 days ago
A love letter to
@nanoporetech.com
pod5lib for reading and writing wire compatible pod5 files in Rust. Compared to the python/C++ library with 50k reads it is: - Read: 1.9 faster and uses ~60x less RAM - Write: 1.7x faster and uses ~5x less RAM
github.com/Psy-Fer/pod5...
crates.io/crates/pod5lib
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GitHub - Psy-Fer/pod5lib-rs: pod5lib in rust
pod5lib in rust. Contribute to Psy-Fer/pod5lib-rs development by creating an account on GitHub.
https://github.com/Psy-Fer/pod5lib-rs
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Interesting that bun now shows up in
@rusttrending.bsky.social
add a skeleton here at some point
about 1 month ago
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Jean P. Elbers
oylenshpeegul
about 1 month ago
Rust was released 11 years ago today. Happy Birthday, Rust!
blog.rust-lang.org/2015/05/15/R...
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Announcing Rust 1.0 | Rust Blog
Empowering everyone to build reliable and efficient software.
https://blog.rust-lang.org/2015/05/15/Rust-1.0/
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Jean P. Elbers
Chenxin Li, PhD
about 1 month ago
Tried it out this morning. It works! I made this phylogeny using Arabidopsis WUS as the query, against a Kalanchoe genome I am working on. The tree reflects known relationships between WUS and WOX paralogs.
add a skeleton here at some point
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Jean P. Elbers
bioRxivpreprint
about 1 month ago
Benchmarking long-read simulators against Oxford Nanopore whole-genome sequencing data
https://www.biorxiv.org/content/10.64898/2026.05.06.723380v1
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Jean P. Elbers
naturepoker
about 1 month ago
Does anyone know if there's written documentation on how ONT put together their dorado bacterial polishing model? I know it fares well on benchmarks, but what is it based on and how did they put it together? Is anyone testing alternate polishing models these days? 💻🧬🧪
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Jean P. Elbers
Philipp Bayer
about 1 month ago
My TEDx talk is online
youtu.be/XX0pgmV1_YA?...
I talk about using detected species to infer undetected species in
#eDNA
!
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How the ghost DNA of fish help protect our oceans | Philipp Bayer | TEDxKingsParkSalon
YouTube video by TEDx Talks
https://youtu.be/XX0pgmV1_YA?si=S1sRvdYCVDvK-ged
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reposted by
Jean P. Elbers
bioRxivpreprint
about 1 month ago
NanoLabel: A fast and accurate real-time nanopore signal classifier
https://www.biorxiv.org/content/10.64898/2026.05.03.722500v1
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sourceforge.net/projects/bbm...
Brian Bushnell and Colleagues are developing DynamicDemi Log methods to rapidly compare genomes instead of more traditional MinHash-like methods. See newer versions of BBMap such as version 39.83
#bbmap
#bbtools
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BBMap
Download BBMap for free. BBMap short read aligner, and other bioinformatic tools. This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pur...
https://sourceforge.net/projects/bbmap/
about 2 months ago
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Jean P. Elbers
Mile Sikic
about 2 months ago
HERRO has been published in
@nature.com
nature.com/articles/s41...
. This achievement is a result of the great work by Dominik Stanojevic, with contributions from Dehui Lin,
@sergeynurk.bsky.social
, and Paola Florez de Sessions Welcome to the era of high-quality genome assemblies supported by AI.
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Telomere-to-Telomere Assembly Using HERRO-Corrected Simplex Nanopore Reads - Nature
Nature - Telomere-to-Telomere Assembly Using HERRO-Corrected Simplex Nanopore Reads
https://nature.com/articles/s41586-026-10563-y
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reposted by
Jean P. Elbers
John Marshall
about 2 months ago
Today's pysam 0.24.0 release bundles htslib, samtools, and bcftools 1.23.1 and has pre-built wheels for Python 3.8 through 3.14. Notably it includes modified_bases fixes thanks to reports by Leszek Pryszcz and Jun Mencius, and new documentation for VariantRecord et al written by
@timd.one
. 🧬🖥️
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Release v0.24.0 · pysam-developers/pysam
This pysam release wraps htslib/samtools/bcftools version 1.23.1 (PR #1343, PR #1372, and PR #1396) and now requires Cython 3. It has been tested with Python versions 3.8 through 3.14, and wheels a...
https://github.com/pysam-developers/pysam/releases/tag/v0.24.0
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reposted by
Jean P. Elbers
GomahuAzarashi
about 2 months ago
#JuliaLang
RustCall.jl is out!
github.com/AtelierArith...
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GitHub - AtelierArith/RustCall.jl: It's the last call for headache.
It's the last call for headache. Contribute to AtelierArith/RustCall.jl development by creating an account on GitHub.
https://github.com/AtelierArith/RustCall.jl
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reposted by
Jean P. Elbers
Michael Hall
about 2 months ago
I took a look at how the new(ish) lr:hq preset in minimap2 impacts variant calling—i.e., if I should move to using it instead of the default map-ont for recent ONT data.
mbhall88.github.io/post/minimap...
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Minimap2 lr:hq preset testing
Evaluating minimap2’s lr:hq preset for bacterial nanopore variant calling Introduction Oxford Nanopore Technologies (ONT) sequencing accuracy has improved dramatically in recent years. With basecallin...
https://mbhall88.github.io/post/minimap2-lrhq-preset-testing/
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Jean P. Elbers
Charlie Gao
about 2 months ago
Just released mori 0.1.0 on CRAN — a new R package for shared memory across processes. Parallel R no longer has to mean duplicating your dataset in every worker's RAM.
opensource.posit.co/blog/2026-04...
🧵 1/3
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mori: Shared memory for R objects
mori is a new R package for sharing R objects across processes via OS-level shared memory. Parallel workers get zero-copy, lazy ALTREP access to the same physical pages — share once, read anywhere.
https://opensource.posit.co/blog/2026-04-23_mori-0-1-0/
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Jean P. Elbers
Stephen Turner
about 2 months ago
Data Science Team Training: Building data science capacity in the public health workforce. I'm writing a (free) e-book for public health practitioners upskilling in data science, as part of my work with the CSTE's DSTT program.
blog.stephenturner.us/p/data-scien...
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Data Science Team Training
Building data science capacity in the public health workforce: A free e-book for public health practitioners upskilling in data science.
https://blog.stephenturner.us/p/data-science-team-training
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reposted by
Jean P. Elbers
David Eccles 🌻🇵🇸7x🩹🛡️
2 months ago
Unfortunately,
@nanoporetech.com
really dropped the ball on the cost aspect by killing their P2 Solo line. Those devices were cheap, and had a low ongoing service / warranty cost, so were ideal for small to medium-scale research labs. PacBio doesn't have anything to target that market either... 🤷♀️.
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Jean P. Elbers
Igor Martayan
2 months ago
Not nearly as polished, but I'm currently writing my thesis and it overlaps many of these topics
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Jean P. Elbers
Ragnar {Groot Koerkamp}
2 months ago
My thesis also covers a bunch of this. Specifically the chapters introducing pairwise alignment and minimizers:
curiouscoding.nl/categories/t...
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Thesis
https://curiouscoding.nl/categories/thesis/
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Looks very cool: fastVEP: A Fast, Comprehensive Variant Effect Predictor Written in Rust
www.biorxiv.org/content/10.6...
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https://www.biorxiv.org/content/10.64898/2026.04.14.718452v1
2 months ago
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Jean P. Elbers
Micah Dunthorn
2 months ago
Quick taxonomic assignment of Nanopore metabarcoding data
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GitHub - frederic-mahe/nf-pore2taxa: quick taxonomic assignment of Nanopore metabarding data
quick taxonomic assignment of Nanopore metabarding data - frederic-mahe/nf-pore2taxa
https://github.com/frederic-mahe/nf-pore2taxa?tab=readme-ov-file
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reposted by
Jean P. Elbers
Chris Miller
2 months ago
What about Computeral Bioinfology?
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Jean P. Elbers
Katharina Hoff
2 months ago
GALBA2 is walking into the arena.
github.com/Gaius-August...
Fully ported to snakemake, accuracy matches old
galba.pl
, similar features as BRAKER4, but smaller containers.
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Jean P. Elbers
Katharina Hoff
2 months ago
GALBA is the short-lived emperor. To our surprise, GALBA is still used. GALBA2 is on his way...
#genomeannotation
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reposted by
Jean P. Elbers
Devin Judge-Lord
2 months ago
Huge gratitude to the open-source community behind
@quarto.org
. With university efforts to improve digital accessibility, it's a great time to switch to Markdown to share class materials in accessible HTML. Here is my template course website if you want to try it:
judgelord.github.io/PP000/
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reposted by
Jean P. Elbers
Katharina Hoff
2 months ago
1/ BRAKER4 hatched! The Earth BioGenome Project is on track to sequence ~1.5M eukaryotic species. Every one needs a structural annotation. No Perl monolith was going to survive that. So we rewrote BRAKER from the ground up.
github.com/Gaius-August...
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Jean P. Elbers
Katharina Hoff
2 months ago
What will it be able to do, the magic & shiny BRAKER4? It’s a story of „You asked, we deliver…“ For example, it will distribute across your HPC. It will run repeat masking. It will annotate noncoding RNAs… stay tuned.
#genomeannotation
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Jean P. Elbers
SquiDBase
5 months ago
The SquiDBase paper has now been published in NAR Genomics and Bioinformatics:
doi.org/10.1093/narg...
SquiDBase (squiggle database) is an open, community-driven resource for raw
#nanopore
sequencing signal data from
#microbial
and
#viral
origin, complemented by corresponding basecalled reads.
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SquiDBase: a community resource of raw nanopore data from microbes
Abstract. Nucleotide sequences in the FASTQ or BAM format are widely shared, yet derived from platform-specific raw data outputs that differ across sequenc
https://doi.org/10.1093/nargab/lqaf213
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Saw this on Twitter/X AppBundler v1.0 transforms any Julia application into a Snap installer (Linux), MSIX (Windows), or DMG (macOS) without leaving the Julia ecosystem, using cross-platform utilities compiled via Yggdrasil.
#JuliaLang
discourse.julialang.org/t/ann-appbun...
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[ANN] AppBundler v1.0: Native Installers for Julia Applications
Packaging a Julia application into a native installer has traditionally meant wrestling with platform-specific tooling on each target system. I am pleased to announce AppBundler v1.0 changes that. Tur...
https://discourse.julialang.org/t/ann-appbundler-v1-0-native-installers-for-julia-applications/136438?u=fabio_sodre
2 months ago
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Ok, now that is one heck of a plotting library!
add a skeleton here at some point
3 months ago
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reposted by
Jean P. Elbers
James Ferguson
3 months ago
Cooking up a cool feature for kuva with --interactive, where it adds a search, and group highlighting and coordinates on mouse, all within the native SVG file, when looking at it with a browser. This is just the minimal working prototype. What do you think?
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Jean P. Elbers
Ragnar {Groot Koerkamp}
3 months ago
Did anybody build a De Bruijn graph on HPRCv2 yet? I'd like to try running sassy against the Eulertigs of the k=31 graph. I see the AGC file is only 3GB, so maybe that allows for an easy way to just get an SPSS out of it?
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Jean P. Elbers
Jim Shaw
3 months ago
Myloasm, our long-read metagenome assembler, is now published! w/
@mgmarin.bsky.social
and
@lh3lh3.bsky.social
Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback.
rdcu.be/famFj
add a skeleton here at some point
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Jean P. Elbers
bioRxiv Bioinfo
3 months ago
Open-source, Hardware-Independent GPU Acceleration for Scalable Nanopore Basecalling with Slorado and Openfish
https://www.biorxiv.org/content/10.64898/2026.03.25.714356v1
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videocardz.com/newz/hp-unve...
wow, 4 Nvidia RTX Pro 6000 Blackwell GPU support. Future Oxford Nanopore attachment for the P48 sequence?
@kirk3gaard.bsky.social
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HP unveils Z8 Fury G6i workstation with quad RTX PRO 6000 Blackwell GPUs offering 384GB VRAM - VideoCardz.com
HP Z8 Fury G6i supports up to four RTX PRO 6000 Blackwell GPUs HP has introduced the Z8 Fury G6i, a new high-end workstation built around Intel’s Xeon 600
https://videocardz.com/newz/hp-unveils-z8-fury-g6i-workstation-with-quad-rtx-pro-6000-blackwell-gpus-offering-384gb-vram
3 months ago
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Jean P. Elbers
Sylvain Wallez
3 months ago
aq: a jq-like tool to query table-oriented data files. Supports Apache Arrow, Parquet, CSV and NDJSON. Written in
#RustLang
by my friend
@anaethelion.bsky.social
github.com/Anaethelion/aq
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GitHub - Anaethelion/aq: jq for Apache Arrow — query Parquet, Arrow IPC, CSV, and NDJSON files using jq-style expressions
jq for Apache Arrow — query Parquet, Arrow IPC, CSV, and NDJSON files using jq-style expressions - Anaethelion/aq
https://github.com/Anaethelion/aq
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