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

Pervasive ancestry bias in variant effect predictors
doi.org/10.1101/2024...

#VariantCalling #Bioinformatics
NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction
Once a suitable reference sequence has been generated, intraspecific variation is often assessed by re-sequencing. Variant calling processes can reveal all differences between strains, accessions, gen...
doi.org
April 6, 2025 at 3:17 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
ecseq.bsky.social
FINAL CALL - 9th Berlin Summer School in NGS Data Analysis 2025 (June 30 - July 4 in Berlin, Germany) - Apply Now 🌐 www.ecseq.com/summer-school

#NGS #BerlinSummerSchool #VariantCalling #Transcriptomics #RNAseq #DNAseq
May 23, 2025 at 2:22 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
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
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
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
molbioevol.bsky.social
New graph-based tool ska lo enables reference-free detection of SNPs, indels, and variant groups from pathogen WGS data. Benchmarking shows high sensitivity, including in regions with dense mutations.

Link: doi.org/10.1093/molb...

#NewPaperAlert #bioinformatics #variantcalling #genomics
Reference-free variant calling with local graph construction with ska lo (SKA)
Abstract. The study of genomic variants is increasingly important for public health surveillance of pathogens. Traditional variant calling methods from who
doi.org
April 10, 2025 at 5:36 PM
dnarnaresearch.bsky.social
Lancet2: Improved and accelerated somatic variant calling with joint multi-sample local assembly graph
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...

#VariantCalling #PopulationGenomics
doi.org
February 24, 2025 at 5:53 AM
commsmed.nature.com
🚨 NEW RESEARCH! ⚕️ 🩺

Bollas et al. introduce VarRNA, a novel classifier of single nucleotide variants and insertions/deletions from tumor transcriptomes using RNA-seq data.

https://bit.ly/460PXmY
#RNAseq #VariantCalling
Variant calling from RNA-Seq data reveals allele-specific differential expression of pathogenic cancer variants - Communications Medicine
Bollas and Gaither et al. present a method to classify simple germline and somatic sequence variants called from tumor RNA sequencing data alone. This machine learning-based approach simplifies variant classification and illustrates the importance of RNA in cancer molecular profiling.
bit.ly
June 20, 2025 at 9:48 AM
plantgenomics.bsky.social
Variant Set Distillation
doi.org/10.1101/2024...

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

#Bioinformatics #NGS #VariantCalling
Variant Set Distillation
Allelic heterogeneity -- the presence of multiple causal variants at a given locus -- has been widely observed across human traits. Combining the association signals across these distinct causal varia...
doi.org
May 28, 2025 at 4:11 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
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
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
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
jsantoyo.bsky.social
A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures. #SomaticVariantDetection #VariantCalling #Pangenomics #Genomics #Bioinformatics @biorxiv-genomic.bsky.social
www.biorxiv.org/content/10.1...
October 21, 2025 at 10:30 AM
jsantoyo.bsky.social
A scalable distributed pipeline for reference-free variants calling. #VariantCalling #ReferenceFreeCalling #Bioinformatics #Genomics #BMCgenomics 🖥️ 🧪
bmcgenomics.biomedcentral.com/articles/10....
A scalable distributed pipeline for reference-free variants calling - BMC Genomics
Background Precision medicine pipelines typically begin with variant calling to identify disease-related mutations for optimal treatment selection. Reference-free approaches assess variations in the…
bmcgenomics.biomedcentral.com
June 5, 2025 at 8:32 AM
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
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
plantgenomics.bsky.social
Blackbird: structural variant detection using synthetic and low-coverage long-reads
doi.org/10.1101/2024...

Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis
doi.org/10.1101/2021...

#VariantCalling #Genomics
Blackbird: structural variant detection using synthetic and low-coverage long-reads
Recent benchmarks of structural variant (SV) detection tools revealed that the majority of human genome structural variations (SVs), especially the medium-range (50-10,000 bp) SVs cannot be resolved w...
doi.org
November 19, 2024 at 5:07 PM
jsantoyo.bsky.social
Learning-based parallel acceleration for HaplotypeCaller. #VariantCalling #HaplotypeCaller #GATK #Genomics #Bioinformatics #BMCbioinformatics 🧬 🖥️
bmcbioinformatics.biomedcentral.com/articles/10....
September 2, 2025 at 9:15 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
plantgenomics.bsky.social
Systematic evaluation of de novo mutation calling tools using whole genome sequencing data
doi.org/10.1101/2024...

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

#Genomics #VariantCalling
Systematic evaluation of de novo mutation calling tools using whole genome sequencing data
De novo mutations (DNMs) are genetic alterations that occur for the first time in an offspring. DNMs have been found to be a significant cause of severe developmental disorders. With the widespread us...
doi.org
June 27, 2025 at 4:50 AM
jsantoyo.bsky.social
Finding easy regions for short-read variant calling from pangenome data. #VariantCalling #HumanGenome #PangenomeData #Bioinformatics #Genomics @gigascience.bsky.social
academic.oup.com/gigascience/...
September 22, 2025 at 1:49 PM
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