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Articles by Anders Jemt
nf-core/raredisease: 2.6.0 - Cacofonix
Published June 25, 2025 | Version 2.6.0 Software Open What's Changed Update SVDB/merge module to fix language server problems by @fellen31 in https://github.com/nf-core/raredisease/pull/684 Replace for loop in create_pedigree_file by @fellen31 in https://github.com/nf-core/raredisease/pull/683 Skip alignment - start from bam files by @kubranarci in https://github.com/nf-core/raredisease/pull/682 Update deepvariant to 1.8.0 by @ramprasadn in https://github.com/nf-core/raredisease/pull/687...
nf-core/raredisease: 2.5.0 - Fulliautomatix
Published May 22, 2025 | Version 2.5.0 Software Open What's Changed concatenate nuclear and mt SNV calls by @ramprasadn in https://github.com/nf-core/raredisease/pull/699 Add Verifybamid2 by @ramprasadn in https://github.com/nf-core/raredisease/pull/701 Patch Vitalstatistix by @ramprasadn in https://github.com/nf-core/raredisease/pull/697 Full Changelog: https://github.com/nf-core/raredisease/compare/2.4.0...2.5.0 Name Size md5:7b7356b14f337d7abcaa7cc31aa7372f 3.4 MB Software:...
nf-core/raredisease: 2.4.0 - Vitalstatistix
Published February 24, 2025 | Version 2.4.0 Software Open What's Changed add markdup to multiqc by @ramprasadn in https://github.com/nf-core/raredisease/pull/679 Full Changelog: https://github.com/nf-core/raredisease/compare/2.3.0...2.4.0 Name Size md5:8e83c2fee657a8390fc01848b9b78ef9 3.3 MB Software: https://github.com/nf-core/raredisease/tree/2.4.0 (URL)
nf-core/raredisease: 2.3.0 - Getafix
What's Changed Bumpversion 2.2.0->2.3.0dev by @ramprasadn in https://github.com/nf-core/raredisease/pull/610 Add option to analyse only mitochondria by @ramprasadn in https://github.com/nf-core/raredisease/pull/608 5% frequency threshold for mitochondrial clinical vcfs by @ramprasadn in https://github.com/nf-core/raredisease/pull/616 allow vep 112 by @jemten in https://github.com/nf-core/raredisease/pull/617 Minor fixes by @ramprasadn in https://github.com/nf-core/raredisease/pull/618 update...
Recommendations for Bioinformatics in Clinical Practice
Abstract Next Generation Sequencing (NGS) is increasingly used in clinical diagnostics, largely driven by the success and robustness of Whole Genome Sequencing (WGS). Whereas updated guidelines exist for how to interpret and report on variants that are identified from NGS using bioinformatics pipelines, there is a need for standardised bioinformatics practices for diagnostics to ensure clinical consensus, accuracy, reproducibility and comparability of the results.
Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics
This study was performed in accordance with the Declaration of Helsinki and current Swedish legislation. The gingival tissue collection was approved by the Regional Ethics Board in Stockholm with reference number 2008/1935 – 31/3 and written informed consent was obtained from all individuals included in the study. Gingival tissue biopsies were collected from subjects with periodontitis and healthy controls without periodontitis as previously described17,32.
Corrigendum: An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries
This Article contains errors in Figure 6c. The Pearson correlation values for the automated and manually prepared samples were inadvertently switched. The correct Figure 6c appears below as Figure 1. This work is licensed under a Creative Commons Attribution 4.0 International License.
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