longcallD is a new variant caller for genomic long reads. It jointly calls phased small and structural variants. Single binary, one command line for the whole process. Comparable accuracy to mainstream callers. Great work by Yan Gao. github.com/yangao07/lon...
GitHub - yangao07/longcallD: A local-haplotagging-based small and structural variant caller
A local-haplotagging-based small and structural variant caller - yangao07/longcallD
github.com
March 24, 2025 at 4:53 PM
longcallD is a new variant caller for genomic long reads. It jointly calls phased small and structural variants. Single binary, one command line for the whole process. Comparable accuracy to mainstream callers. Great work by Yan Gao. github.com/yangao07/lon...
New preprint from the team #AdaptiveIntrogression #Haplotagging #PopGen #MarEvol
"Adaptive introgression in subdivided populations leaves distinct genomic footprints under global and local selection: a case study in Ciona intestinalis"
www.biorxiv.org/content/10.6...
"Adaptive introgression in subdivided populations leaves distinct genomic footprints under global and local selection: a case study in Ciona intestinalis"
www.biorxiv.org/content/10.6...
Adaptive introgression in subdivided populations leaves distinct genomic footprints under global and local selection: a case study in Ciona intestinalis
Adaptive introgression, the transfer of beneficial alleles between species through hybridization, is increasingly recognized as an important source of adaptation to novel environments. However, the th...
www.biorxiv.org
October 4, 2026 at 10:19 PM
New preprint from the team #AdaptiveIntrogression #Haplotagging #PopGen #MarEvol
"Adaptive introgression in subdivided populations leaves distinct genomic footprints under global and local selection: a case study in Ciona intestinalis"
www.biorxiv.org/content/10.6...
"Adaptive introgression in subdivided populations leaves distinct genomic footprints under global and local selection: a case study in Ciona intestinalis"
www.biorxiv.org/content/10.6...
Harpy: a pipeline for processing haplotagging linked-read data academic.oup.com/bioinformati... 🧬🖥️🧪
code github.com/pdimens/harpy
docs pdimens.github.io/harpy/
code github.com/pdimens/harpy
docs pdimens.github.io/harpy/
June 18, 2025 at 3:30 PM
Harpy: a pipeline for processing haplotagging linked-read data academic.oup.com/bioinformati... 🧬🖥️🧪
code github.com/pdimens/harpy
docs pdimens.github.io/harpy/
code github.com/pdimens/harpy
docs pdimens.github.io/harpy/
But here's where it gets awesomer. You can set up a GH repo to automatically build your notebooks into a *nice* website (via JupyterBook). Your repository, your work, code, results, and narrative *as a website*. Automatically. Automagically. The sims project? pdimens.github.io/haplotagging...
Linked Read Inversion Detection Performance Simulations - Inversion Simulations
The code and data exploration of the D. melanogaster haplotagging simulation experiment
pdimens.github.io
February 26, 2025 at 3:32 PM
But here's where it gets awesomer. You can set up a GH repo to automatically build your notebooks into a *nice* website (via JupyterBook). Your repository, your work, code, results, and narrative *as a website*. Automatically. Automagically. The sims project? pdimens.github.io/haplotagging...
🧬 Explore the latest from Bioinformatics Advances: “Harpy: A pipeline for processing haplotagging linked-read data”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf133
Authors include: @pvdimens.bsky.social
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf133
Authors include: @pvdimens.bsky.social
June 18, 2025 at 10:02 AM
🧬 Explore the latest from Bioinformatics Advances: “Harpy: A pipeline for processing haplotagging linked-read data”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf133
Authors include: @pvdimens.bsky.social
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf133
Authors include: @pvdimens.bsky.social
2- We tested this prediction in a well-characterized case of adaptive introgression, in the sea squirt Ciona intestinalis:
Using haplotagging and local ancestry, we find no correlation between allele frequency and tract length, supporting local adaptation.
Using haplotagging and local ancestry, we find no correlation between allele frequency and tract length, supporting local adaptation.
October 4, 2026 at 10:19 PM
2- We tested this prediction in a well-characterized case of adaptive introgression, in the sea squirt Ciona intestinalis:
Using haplotagging and local ancestry, we find no correlation between allele frequency and tract length, supporting local adaptation.
Using haplotagging and local ancestry, we find no correlation between allele frequency and tract length, supporting local adaptation.
Harpy v1.0 is officially out and... YOU DON'T NEED DATA. You read that right, you don't need data to get started. It now includes a genomic variant and linked-read simulator, so all you need is a haploid genome and you can simulate the rest to try out haplotag analysis 😁
github.com/pdimens/HARPY
github.com/pdimens/HARPY
GitHub - pdimens/harpy: Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included.
Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included. - pdimens/harpy
github.com
June 5, 2024 at 6:43 PM
Harpy v1.0 is officially out and... YOU DON'T NEED DATA. You read that right, you don't need data to get started. It now includes a genomic variant and linked-read simulator, so all you need is a haploid genome and you can simulate the rest to try out haplotag analysis 😁
github.com/pdimens/HARPY
github.com/pdimens/HARPY
Fantastic work by the DeepVariant team!
Local read haplotagging enables accurate long-read small variant calling www.biorxiv.org/content/10.1...
Local read haplotagging enables accurate long-read small variant calling www.biorxiv.org/content/10.1...
Local read haplotagging enables accurate long-read small variant calling
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
September 18, 2023 at 2:42 PM
Fantastic work by the DeepVariant team!
Local read haplotagging enables accurate long-read small variant calling www.biorxiv.org/content/10.1...
Local read haplotagging enables accurate long-read small variant calling www.biorxiv.org/content/10.1...
This haplotagging method is not based on 10x, it is DIY. It is also cheap.
August 30, 2025 at 12:36 PM
This haplotagging method is not based on 10x, it is DIY. It is also cheap.
Harpy is a modular, user-friendly pipeline for analyzing haplotagging linked-read sequencing data.
June 18, 2025 at 10:02 AM
Harpy is a modular, user-friendly pipeline for analyzing haplotagging linked-read sequencing data.
Oh hey, the Harpy paper is out. The software's been available, but it's nice to have something in writing! It also works with other linked read data and non-linked data (wgs, rad) 😁
@bioinfoadv.bsky.social on Bluesky
🧬 Explore the latest from Bioinformatics Advances: “Harpy: A pipeline for processing haplotagging linked-read data”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf133
Authors include: @pvdimens.bsky.social
bsky.app
June 18, 2025 at 11:29 AM
Oh hey, the Harpy paper is out. The software's been available, but it's nice to have something in writing! It also works with other linked read data and non-linked data (wgs, rad) 😁
Iris Jia (Valle) is a PhD student at the University of New Brunswick Saint John 🇨🇦 exploring #genomic differences in #AtlanticBluefinTuna populations.
She uses recently developed tools like #haplotagging to investigate how #genes are affecting recovery and migratory behavior.
She uses recently developed tools like #haplotagging to investigate how #genes are affecting recovery and migratory behavior.
April 2, 2026 at 1:44 PM
Iris Jia (Valle) is a PhD student at the University of New Brunswick Saint John 🇨🇦 exploring #genomic differences in #AtlanticBluefinTuna populations.
She uses recently developed tools like #haplotagging to investigate how #genes are affecting recovery and migratory behavior.
She uses recently developed tools like #haplotagging to investigate how #genes are affecting recovery and migratory behavior.
I am looking to fill a 54-months (!) lead research technician position, working on my #ERC project, developing haplotagging methods, managing data and helping with field work. More information here :
euraxess.ec.europa.eu/jobs/225940
Exciting opportunity in Paris!
Please RT!
#evolution #genetics
euraxess.ec.europa.eu/jobs/225940
Exciting opportunity in Paris!
Please RT!
#evolution #genetics
April 17, 2024 at 9:36 AM
I am looking to fill a 54-months (!) lead research technician position, working on my #ERC project, developing haplotagging methods, managing data and helping with field work. More information here :
euraxess.ec.europa.eu/jobs/225940
Exciting opportunity in Paris!
Please RT!
#evolution #genetics
euraxess.ec.europa.eu/jobs/225940
Exciting opportunity in Paris!
Please RT!
#evolution #genetics
Oh hey, Harpy v1.11 is out! 🎉😁
Why does that matter? De novo assembly workflows now included!!! (regular and metagenome)
(and bug fixes, optimizations, lots more guardrails)
github.com/pdimens/HARPY
Why does that matter? De novo assembly workflows now included!!! (regular and metagenome)
(and bug fixes, optimizations, lots more guardrails)
github.com/pdimens/HARPY
GitHub - pdimens/harpy: Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included.
Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included. - pdimens/harpy
github.com
November 11, 2024 at 5:53 PM
Oh hey, Harpy v1.11 is out! 🎉😁
Why does that matter? De novo assembly workflows now included!!! (regular and metagenome)
(and bug fixes, optimizations, lots more guardrails)
github.com/pdimens/HARPY
Why does that matter? De novo assembly workflows now included!!! (regular and metagenome)
(and bug fixes, optimizations, lots more guardrails)
github.com/pdimens/HARPY
#Haplotagging now enables researchers to quickly and precisely trace and match #genome data - with surprising results about butterfly patterns! Read the full story here: https://tuebingen.mpg.de/en/detail/haplotagging0/ Exciting news, @frankyc1101, @mel_rosina, @joana_meier,...
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tuebingen.mpg.de
November 22, 2024 at 8:40 PM
#Haplotagging now enables researchers to quickly and precisely trace and match #genome data - with surprising results about butterfly patterns! Read the full story here: https://tuebingen.mpg.de/en/detail/haplotagging0/ Exciting news, @frankyc1101, @mel_rosina, @joana_meier,...
@ERC_Research grant "Proof of Concept" for an ambitious study at the Friedrich Miescher Laboratory in Tübingen lead by @frankyc1101 to generate high quality genome datasets from 2000 people with #haplotagging. Congratulations! Read more: https://sohub.io/uu64 #Genomesequencing
November 22, 2024 at 6:28 PM
@ERC_Research grant "Proof of Concept" for an ambitious study at the Friedrich Miescher Laboratory in Tübingen lead by @frankyc1101 to generate high quality genome datasets from 2000 people with #haplotagging. Congratulations! Read more: https://sohub.io/uu64 #Genomesequencing
github.com/yangao07/lon... variant caller foe long reads.
GitHub - yangao07/longcallD: A local-haplotagging-based small and structural variant caller
A local-haplotagging-based small and structural variant caller - yangao07/longcallD
github.com
March 24, 2025 at 5:56 PM
github.com/yangao07/lon... variant caller foe long reads.
Haplotagging?
www.pnas.org/doi/abs/10.1...
www.pnas.org/doi/abs/10.1...
Haplotype tagging reveals parallel formation of hybrid races in two butterfly species | PNAS
Genetic variation segregates as linked sets of variants or haplotypes. Haplotypes
and linkage are central to genetics and underpin virtually all ge...
www.pnas.org
August 27, 2025 at 8:55 PM
Haplotagging?
www.pnas.org/doi/abs/10.1...
www.pnas.org/doi/abs/10.1...
Local read haplotagging enables accurate long-read small variant calling https://www.biorxiv.org/content/10.1101/2023.09.07.556731v1
Local read haplotagging enables accurate long-read small variant calling https://www.biorxiv.org/content/10.1101/2023.09.07.556731v1
Long-read sequencing technology has enabled variant detection in difficult-to-map regions of the gen
www.biorxiv.org
September 12, 2023 at 11:49 AM
Local read haplotagging enables accurate long-read small variant calling https://www.biorxiv.org/content/10.1101/2023.09.07.556731v1
Local read haplotagging enables accurate long-read small variant calling https://www.biorxiv.org/content/10.1101/2023.09.07.556731v1
Local read haplotagging enables accurate long-read small variant calling https://www.biorxiv.org/content/10.1101/2023.09.07.556731v1
Long-read sequencing technology has enabled variant detection in difficult-to-map regions of the gen
www.biorxiv.org
September 12, 2023 at 11:49 AM
Local read haplotagging enables accurate long-read small variant calling https://www.biorxiv.org/content/10.1101/2023.09.07.556731v1
The project will also work with @frankyc1101 to apply haplotagging sequencing technology to understand the polymorphism
December 19, 2024 at 2:05 PM
The project will also work with @frankyc1101 to apply haplotagging sequencing technology to understand the polymorphism