ArticleNAR genomics and bioinformatics2024
Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery.
Article in NAR genomics and bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
- Neoadjuvant ipilimumab plus nivolumab in melanoma: 5-year survival and biomarker analysis from the phase 2 PRADO-trial.Nature medicine · 2026Trial
- T-rex: standardized analysis of germline variants in whole-exome sequencing trios.Scientific reports · 2026Article
- Genomic Dissection of Growth Traits and Spatial Independence from Breed-Defining Loci in Jining Grey Goats.Animals : an open access journal from MDPI · 2026Article
- Chronic interferon signaling at baseline is associated with acquired resistance to immunotherapy in metastatic melanoma.Cell reports. Medicine · 2026Article
- Multi-omic characterization of 14q deletion in renal clear cell carcinoma identifiesJournal for immunotherapy of cancer · 2026Article
- Case of complete response to immunotherapy in MMR-deficient prostate cancer associated with NK-like and CD4Cell reports. Medicine · 2026Article
- Dissecting cancer in a non-mammalian model: genomic insights from lemon frost geckos.BMC biology · 2026Article
- Exploring per-base quality scores as a surrogate marker of cell-free DNA fragmentome.Briefings in bioinformatics · 2026Article
- MuSA: a Nextflow pipeline for deep, reproducible annotation and clinical ranking of genomic variants.BMC bioinformatics · 2026Article
- Whole-genome sequencing with AVITI and NovaSeq X Plus reveals comparable performance with contextual biases.NAR genomics and bioinformatics · 2026Article
- A 15-layer multi-omics analysis of gastric cancer ecotypes provides therapeutic insights.Cell reports. Medicine · 2026Article
- DIAG: A Framework for Evaluating Whole-Genome Amplification Quality in Single-Cell SNV Analysis.Biology · 2026Article
- Genomic Profiling of Adults with Pharmacoresistant Genetic Generalized Epilepsy.Brain sciences · 2026Article
- Discovery and characterization of gene-by-environment and epistatic genetic effects in a vertebrate model.Cell genomics · 2026Article
- Article
- Fifteen Years of the Genome Analysis Toolkit as the De Facto Standard in Short-Read Variant Calling.International journal of molecular sciences · 2026Review
- Rare regulatory mutations disrupt mesenchymal molecular programs driving endocardial cushion formation in bicuspid aortic valve.Nature communications · 2026Article
- WeavePop: a bioinformatics workflow to explore and analyze genomic variants of eukaryotic populations.G3 (Bethesda, Md.) · 2026Article
- Somatic copy number alterations profiling in non-small cell lung cancer and their correlation with clinical efficacy in first-line treatment.Genome medicine · 2026Article
- Spatial single cell transcriptomic analysis informs tumor developmental hierarchy of DICER1 syndrome related sarcoma.Nature communications · 2026Article
2 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA variation analysis has become indispensable in many aspects of modern biomedicine, most prominently in the comparison of normal and tumor samples. Thousands of samples are collected in local sequencing efforts and public databases requiring highly scalable, portable, and automated workflows for streamlined processing. Here, we present nf-core/sarek 3, a well-established, comprehensive variant calling and annotation pipeline for germline and somatic samples. It is suitable for any genome with a known reference. We present a full rewrite of the original pipeline showing a significant reduction of storage requirements by using the CRAM format and runtime by increasing intra-sample parallelization. Both are leading to a 70% cost reduction in commercial clouds enabling users to do large-scale and cross-platform data analysis while keeping costs and CO
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.