ArticleF1000Research2020
Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants.
Article in F1000Research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 185 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
185 citing papers in PubMed.
- Neoadjuvant palbociclib and endocrine therapy versus chemotherapy in ER + /HER2- breast cancer: a randomized phase II trial.Nature communications · 2026Trial
- Trial
- Immunological biomarkers of response and resistance to treatment with cabozantinib and nivolumab in recurrent endometrial cancer.Journal for immunotherapy of cancer · 2025Trial
- Ipilimumab and nivolumab combined with anthracycline-based chemotherapy in metastatic hormone receptor-positive breast cancer: a randomized phase 2b trial.Journal for immunotherapy of cancer · 2024Trial
- Atezolizumab plus anthracycline-based chemotherapy in metastatic triple-negative breast cancer: the randomized, double-blind phase 2b ALICE trial.Nature medicine · 2022Trial
- Article
- Article
- Exome sequencing points to pathogenic ATM variants in gastric cancer.European journal of human genetics : EJHG · 2026Article
- Somatic likelihood tiering: an interpretable post-calling triage protocol for tumor-only whole-exome variant review.Briefings in bioinformatics · 2026Article
- Deep tissue sequencing improves genetic diagnostic yield in focal cortical dysplasia.Progress in neuro-psychopharmacology & biological psychiatry · 2026Article
- Clonal hematopoiesis of indeterminate potential and metabolic dysfunction-associated steatotic liver disease: Korean biopsy cohort.Hepatology international · 2026Article
- Multiomic profiling links L1 retrotransposition to genomic instability and ecDNA in bladder cancer.Nature communications · 2026Article
- Dissecting cancer in a non-mammalian model: genomic insights from lemon frost geckos.BMC biology · 2026Article
- Combinatorial Targeting of Avapritinib-Driven MAP Kinase Activation in High-Grade Glioma.Research square · 2026Article
- Enrichment of mutated DNA enables ultra-sensitive ctDNA detection in NSCLC using shallow targeted sequencing.Scientific reports · 2026Article
- Whole-genome sequencing with AVITI and NovaSeq X Plus reveals comparable performance with contextual biases.NAR genomics and bioinformatics · 2026Article
- Beyond chromatin accessibility: bulk ATAC-seq as an integrative assay to portray genomes and epigenomes.NAR genomics and bioinformatics · 2026Article
- Ferroptosis-based therapeutic strategy targeting iron metabolism and SLC7A11 overcomes oxaliplatin resistance in patient-derived pancreatic cancer organoids.Journal of experimental & clinical cancer research : CR · 2026Article
- A 15-layer multi-omics analysis of gastric cancer ecotypes provides therapeutic insights.Cell reports. Medicine · 2026Article
- Reprogramming T cell-myeloid crosstalk overcomes immune resistance in colorectal cancer.Cell reports. Medicine · 2026Article
125 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole-genome sequencing (WGS) is a fundamental technology for research to advance precision medicine, but the limited availability of portable and user-friendly workflows for WGS analyses poses a major challenge for many research groups and hampers scientific progress. Here we present Sarek, an open-source workflow to detect germline variants and somatic mutations based on sequencing data from WGS, whole-exome sequencing (WES), or gene panels. Sarek features (i) easy installation, (ii) robust portability across different computer environments, (iii) comprehensive documentation, (iv) transparent and easy-to-read code, and (v) extensive quality metrics reporting. Sarek is implemented in the Nextflow workflow language and supports both Docker and Singularity containers as well as Conda environments, making it ideal for easy deployment on any POSIX-compatible computers and cloud compute environments. Sarek follows the GATK best-practice recommendations for read alignment and pre-processing, and includes a wide range of software for the identification and annotation of germline and somatic single-nucleotide variants, insertion and deletion variants, structural variants, tumour sample purity, and variations in ploidy and copy number. Sarek offers easy, efficient, and reproducible WGS analyses, and can readily be used both as a production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups. The Sarek source code, documentation and installation instructions are freely available at https://github.com/nf-core/sarek and at https://nf-co.re/sarek/.
Indexed as
Identifiers
What OpenQuestion holds
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.