#VariantCalling
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antobeck.bsky.social
@medrxivpreprint.bsky.social on early access data generated by Baylor College of Medicine scientists with Illumina Constellation Mapped Read Technology. #genomics #VariantCalling #DRAGEN #Constellation bit.ly/48wm3I3
November 25, 2025 at 6:00 AM
jsantoyo.bsky.social
Wgatools: an ultrafast toolkit for manipulating whole genome alignments. #WholeGenomeAlignment #Genomics #LongReads #Sequencing #VariantCalling #DataStructure #Bioinformatics #Rus 🧬 🖥️
academic.oup.com/bioinformati...
Wgatools: an ultrafast toolkit for manipulating whole genome alignments
AbstractSummary. With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed
academic.oup.com
April 5, 2025 at 10:56 AM
trinobia.bsky.social
1/
Still a great intro to genomic surveillance:

cambiotraining.github.io/sars-cov-2-g...

#Trinobia #Bioinformatics #Genomics #NGS #GenomicSurveillance #Phylogenetics #Nextstrain #VariantCalling #ComputationalBiology #LifeSciences #Biotech #Research #Science #DataScience #MolecularBiology
SARS Genomic Surveillance
cambiotraining.github.io
June 7, 2026 at 6:05 PM
clementsui.bsky.social
#WGS #Bacteria #genomics #variantcalling
www.biorxiv.org/content/10.1...
Are reads required? High-precision variant calling from bacterial genome assemblies
Accurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared...
www.biorxiv.org
February 28, 2025 at 4:01 PM
puckerlabpapers.bsky.social
NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction
doi.org/10.1371/jour...

#Bioinformatics #VariantCalling #VariantAnnotation #FunctionalGenomics #Genomics #PlantSci #DataScience #OpenData #OpenAccess #BigData #Python #100DaysOfCode
NAVIP: Unraveling the influence of neighboring small sequence variants on functional impact prediction
Once a suitable reference sequence has been generated, intra-species variation is often assessed by re-sequencing. Variant calling processes can reveal all differences between strains, accessions, gen...
doi.org
July 26, 2025 at 10:08 PM
puckerlab.bsky.social
🧬🔍 Introducing NAVIP – a new tool for predicting variant impacts more accurately! Unlike traditional methods, NAVIP considers the effect of neighboring variants within coding sequences:
doi.org/10.1371/jour...
#Genomics #Bioinformatics #VariantCalling 30/🧵
NAVIP: Unraveling the influence of neighboring small sequence variants on functional impact prediction
Once a suitable reference sequence has been generated, intra-species variation is often assessed by re-sequencing. Variant calling processes can reveal all differences between strains, accessions, gen...
doi.org
March 2, 2025 at 6:25 AM
ergabiodiv.bsky.social
💡 #KnowledgeHighlight | Course: Methods in genomic variant calling by @embl.org @training.ebi.embl.org
🧬 🖥️
www.ebi.ac.uk/training/eve...

Explore open-access training materials in the ERGA #KnowledgeHub ➡️ knowledge.erga-biodiversity.eu #variantcalling #genomics #bioinformatics
February 9, 2026 at 8:30 AM
djosergenomics.github.io
🚀New Blog Post!

Just finished a training project on variant calling using zebrafish data from @uofglasgow.bsky.social study on fisheries selection (PRJNA630223)

Walked through the full pipeline: QC → alignment → variant calling → VEP annotation

#Genomics #Zebrafish #Bioinformatics #VariantCalling
Discovering Mutations in fisheries-induced Selection of Zebrafish
Zebrafish Variant Calling Training Project
djosergenomics.github.io
July 23, 2025 at 12:27 AM
bpucker.bsky.social
Excited to share that NAVIP has been published in @plos.org Computational Biology! 🎉 If you work with sequence variants, give it a read:

doi.org/10.1371/jour...

#Genomics #VariantCalling
@puckerlab.bsky.social @tubraunschweig.bsky.social
NAVIP: Unraveling the influence of neighboring small sequence variants on functional impact prediction
Once a suitable reference sequence has been generated, intra-species variation is often assessed by re-sequencing. Variant calling processes can reveal all differences between strains, accessions, gen...
doi.org
February 20, 2025 at 5:46 PM
medhat.bsky.social
5/ Big thanks to @sedlazeck.bsky.social and Daniel Agustinho for their support and insight on this work!

Would love to hear your thoughts, feedback, or what tools you are using in your long-read work. 👇

#Genomics #Bioinformatics #PacBio #Nanopore #VariantCalling #GenomeAssembly #T2T #Epigenetics
May 5, 2025 at 2:10 PM
jsantoyo.bsky.social
SurVIndel2: improving copy number variant calling from next-generation sequencing using hidden split reads. #CNV #VariantCalling #Genomics @naturecomms.bsky.social 🧬 🖥️
www.nature.com/articles/s41...
SurVIndel2: improving copy number variant calling from next-generation sequencing using hidden split reads - Nature Communications
Copy number variants (CNVs) are the most common structural variants in human genomes however detecting them using short read sequencing is challenging. Here the authors introduce a method that uses a ...
www.nature.com
December 20, 2024 at 10:32 PM
pg-pi3gey.bsky.social
Ok so this #deepvariant caller update from #google is BIG.
github.com/google/deepv...

- 1.6x time reduction (40% increase ??)
- Pangenome integration
- New model and improvements over previously model

Excited to try this new update 🧬💻

#bioinformatics #wgs #ngs #variantcalling
Release DeepVariant 1.8.0 · google/deepvariant
In this release: Small model integration: Speed increased by ~1.7x (40% runtime reduction) for WGS, PacBio, and ONT by introduction of additional small model. The small model identifies easy-to-...
github.com
December 9, 2024 at 6:39 AM
flalom.bsky.social
🧬 Just released vcf-reformatter: A fast Rust tool for flattening VCF files with VEP annotations into TSV format! Ready to work with R/Py
Github: github.com/flalom/vcf-r...
- 🐛 Found a bug? github.com/flalom/vcf-r...
#bioinformatics #rust #vcf #genomics #opensource #variantcalling #cancer_research
July 17, 2025 at 7:48 AM
jsantoyo.bsky.social
The Scalable Variant Call Representation: Enabling Genetic Analysis Beyond One Million Genomes. #VariantCalling #VCF #ScalableVariantCall #SVCR #Genomics #Bioinformaitcs 🧬 🖥️
academic.oup.com/bioinformati...
The Scalable Variant Call Representation: Enabling Genetic Analysis Beyond One Million Genomes
AbstractMotivation. The Variant Call Format (VCF) is widely used in genome sequencing but scales poorly. For instance, we estimate a 150,000 genome VCF wou
academic.oup.com
January 6, 2025 at 8:19 PM
jsantoyo.bsky.social
Clair3-RNA: A deep learning-based small variant caller for long-read RNA sequencing data. #LongReadRNAseq #VariantCalling #DeepLearning #Sequencing #Bioinformatics 🧬 🖥️
www.biorxiv.org/content/10.1...
Clair3-RNA: A deep learning-based small variant caller for long-read RNA sequencing data
Variant calling using long-read RNA sequencing (lrRNA-seq) can be applied to diverse tasks, such as capturing full-length isoforms and gene expression profiling. It poses challenges, however, due to h...
www.biorxiv.org
November 20, 2024 at 1:04 PM
jsantoyo.bsky.social
A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material. #LowFrequencyVariants #SomaticMosaicism #SomaticVariants #VariantCalling #ReferenceMaterials #GiAB #Benchmarking #Genomics 🧬 🖥️ @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
Source: https://www.biorxiv.org/content/10.1101/2024.12.02.625685v1.full.pdf
December 11, 2024 at 8:35 PM
plantgenomics.bsky.social
Complex structural variant visualization with SVTopo
doi.org/10.1101/2025...

Comparison of read mapping and variant calling tools for the analysis of plant NGS data
doi.org/10.1101/2020...

#Genomics #VariantCalling #DataAnalysis
Complex structural variant visualization with SVTopo
Structural variants are genomic variants that impact at least 50 nucleotides and can play major roles in diversity and human health. Many structural variants are complex multi-breakpoint rearrangement...
doi.org
April 23, 2025 at 6:45 PM
gpbees.bsky.social
📄 Variant Calling in the Dark Genome: Benchmarking SNV Calls in the Flanks of Structural Variants

academic.oup.com/gpb/advance-...
#Genomics #VariantCalling #StructuralVariants #Bioinformatics #LongReadSequencing #HumanGenomics 6/6
Validate User
academic.oup.com
September 11, 2026 at 7:30 AM
jsantoyo.bsky.social
Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic. #SomaticVariants #ShortReads #LongReads #VariantCalling #Genomics #Bioinformatics #ToolsBenchmarking #ReferenceDatasets @natbiotech.nature.com 🧬 🖥️
www.nature.com/articles/s41...
October 17, 2025 at 9:15 AM
ghga.bsky.social
Want to improve your genomic variant calling pipeline? Join our webinar to learn about ncbench, a powerful benchmarking tool. We'll also cover other essential genomic benchmarking topics. Register for free: t1p.de/o4al3 🧬🔬 #bioinformatics #genomics #variantcalling #ncbench
Image is a digitally created announcement card in the GHGA colors, dark green and orange. The text reads "Benchmarking and quality control for genomic variant calling, 10.04. 2025, 15:00 CEST" below is a photo of the speaker and his name, Johannes Köster.
March 27, 2025 at 8:14 AM
completegenomics.bsky.social
New study demonstrates up to 73% reduction in genome analysis errors using AI-trained models versus standard approaches

www.completegenomics.com/new-study-de...

#Genomics #WholeGenomeSequencing #VariantCalling #AIinGenomics
#DeepVariant #Pangenome #DNBSEQT7plus #NGS
April 29, 2026 at 9:55 PM
antobeck.bsky.social
Great work out of the #illumina Artificial Intelligence Labs pubklised in @science.org today. PromotorAI to help call variants in non-coding promoter regions of genes. #DRAGEN #GeneRegulation #VariantCalling #WES #WGS
gnovakovsky.bsky.social Gherman Novakovsky @gnovakovsky.bsky.social · May 29
Excited to share my first contribution here at Illumina! We developed PromoterAI, a deep neural network that accurately identifies non-coding promoter variants that disrupt gene expression.🧵 (1/)
May 30, 2025 at 3:55 AM
ecseq.bsky.social
🧬 NGS data is everywhere.

Learn how to analyze it.

Hands-on workshops for life scientists:
🌐 www.ecseq.com/ngs-workshops

#NGS #Bioinformatics #Genomics #RNAseq #DNAseq #VariantCalling #LifeSciences #MolecularBiology #BiomedicalResearch #PrecisionMedicine #Biotech #ScienceTraining
June 11, 2026 at 1:55 PM
plantgenomics.bsky.social
Allele Specific Expression Quality Control Fills Critical Gap in Transcriptome Assisted Rare Variant Interpretation
doi.org/10.1101/2025...

NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction
doi.org/10.1101/596718

#Bioinformatics #VariantCalling
doi.org
June 12, 2025 at 10:08 PM
botsocamerica.bsky.social
From #AppsPlantSci's upcoming #Polyploidy issue🌿

Variant calling in polyploids for population and quantitative genetics -- a review of challenges & solutions, by Alyssa Phillips

bsapubs.onlinelibrary.wiley.com/doi/full/10.... #variantcalling #botany #plantjoy
The graphic shows how read mapping and the called allele dosage in allo- and autopolyploids differ due to the structure of the reference genome. Reads (gray) are shown aligning the reference genome (black), with alleles for the focal variant in pink or yellow. (A) In an allotetraploid with two subgenomes (subgenome K in light gray and subgenome N in dark gray), reads are mapped to one haplotype of each parental subgenome, and diploid genotypes are called. (B) In an autotetraploid with no preferential pairing, all reads are mapped to a single haplotype. Here, reads are aligned to a haplotype carrying the yellow A allele at the focal variant.
July 19, 2024 at 3:38 PM