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: https://doi.org/10.1093/molbev/msaf077

#NewPaperAlert #bioinformatics #variantcalling #genomics

Pipeline release! nf-core/rnavar v1.1.0 - nf-core/rnavar 1.1.0 - Mighty Milano!

Please see the changelog: https://github.com/nf-core/rnavar/releases/tag/1.1.0

#gatk4 #rna #rnaseq #variantcalling #worflow #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/variantbenchmarking v1.2.0 - 1.2.0 Doubtful Adams!

Please see the changelog: https://github.com/nf-core/variantbenchmarking/releases/tag/1.2.0

#benchmark #draft #structuralvariants #variantcalling #nfcore #openscience #nextflow #bioinformatics

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: https://t1p.de/o4al3 🧬🔬 #bioinformatics #genomics #variantcalling #ncbench

I didn't know #Google has #genomics projects. Today I learned

https://github.com/google/deepvariant

#genomics #deeplearning #variantcalling #neuralnetworks

Pipeline release! nf-core/variantbenchmarking v1.1.0 - 1.1.0 Dark Murakami!

Please see the changelog: https://github.com/nf-core/variantbenchmarking/releases/tag/1.1.0

#benchmark #draft #structuralvariants #variantcalling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/pacvar v1.0.1 - v1.0.1 - Sardine [3/6/2025]!

Please see the changelog: https://github.com/nf-core/pacvar/releases/tag/1.0.1

#alignment #longread #pacbio #puretarget #variantcalling #wgs #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/raredisease v2.4.0 - 2.4.0 - Vitalstatistix!

Please see the changelog: https://github.com/nf-core/raredisease/releases/tag/2.4.0

#diagnostics #raredisease #snv #structuralvariants #variantannotation #variantcalling #wes #wgs #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/variantbenchmarking v1.0.0 - Innocent Pamuk

Please see the changelog: https://github.com/nf-core/variantbenchmarking/releases/tag/1.0.0

#benchmark #draft #structuralvariants #variantcalling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.5.1 - 3.5.1 - Akkatjåkkå!

Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.5.1

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/raredisease v2.3.0 - 2.3.0 - Getafix!

Please see the changelog: https://github.com/nf-core/raredisease/releases/tag/2.3.0

#diagnostics #raredisease #snv #structuralvariants #variantannotation #variantcalling #wes #wgs #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/pacvar vv1.0.0 - nf-core/pacvarv1.0.0 - Goldfish [2/05/2024]!

Please see the changelog: https://github.com/nf-core/pacvar/releases/tag/v1.0.0

#alignment #longread #pacbio #puretarget #variantcalling #wgs #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.5.0 - 3.5.0 - Áhkájiegna!

Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.5.0

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

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: https://t1p.de/iz7ob 🧬🔬 #bioinformatics #genomics #variantcalling #ncbench

How do y'all handle primary and alternate #genome #assemblies for downstream analyses? What do you do about #annotation, #VariantCalling etc? What best practices are there?

#genomics #GenomeAssembly