ArticleBMC genomics2017
XCAVATOR: accurate detection and genotyping of copy number variants from second and third generation whole-genome sequencing experiments.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 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
15 citing papers in PubMed.
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Full-length transcriptome profiling ofPhysiology and molecular biology of plants : an international journal of functional plant biology · 2024Article
- On the core segmentation algorithms of copy number variation detection tools.Briefings in bioinformatics · 2024Article
- RegCFinder: targeted discovery of genomic subregions with differential read density.Bioinformatics advances · 2023Article
- Beta Human Papillomavirus 8 E6 Induces Micronucleus Formation and Promotes Chromothripsis.Journal of virology · 2022Article
- Identification of Copy Number Alterations from Next-Generation Sequencing Data.Advances in experimental medicine and biology · 2022Article
- Independent somatic evolution underlies clustered neuroendocrine tumors in the human small intestine.Nature communications · 2021Article
- A Cluster-Based Approach for the Discovery of Copy Number Variations From Next-Generation Sequencing Data.Frontiers in genetics · 2021Article
- Hierarchical discovery of large-scale and focal copy number alterations in low-coverage cancer genomes.BMC bioinformatics · 2020Article
- Genome sequencing in cytogenetics: Comparison of short-read and linked-read approaches for germline structural variant detection and characterization.Molecular genetics & genomic medicine · 2020Article
- RKDOSCNV: A Local Kernel Density-Based Approach to the Detection of Copy Number Variations by Using Next-Generation Sequencing Data.Frontiers in genetics · 2020Article
- MFCNV: A New Method to Detect Copy Number Variations From Next-Generation Sequencing Data.Frontiers in genetics · 2020Article
- A Density Peak-Based Method to Detect Copy Number Variations From Next-Generation Sequencing Data.Frontiers in genetics · 2020Article
- Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines.BMC medical genomics · 2019Article
- Location of Balanced Chromosome-Translocation Breakpoints by Long-Read Sequencing on the Oxford Nanopore Platform.Frontiers in genetics · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWe developed a novel software package, XCAVATOR, for the identification of genomic regions involved in copy number variants/alterations (CNVs/CNAs) from short and long reads whole-genome sequencing experiments.
resultsBy using simulated and real datasets we showed that our tool, based on read count approach, is capable to predict the boundaries and the absolute number of DNA copies CNVs/CNAs with high resolutions. To demonstrate the power of our software we applied it to the analysis Illumina and Pacific Bioscencies data and we compared its performance to other ten state of the art tools.
conclusionAll the analyses we performed demonstrate that XCAVATOR is capable to detect germline and somatic CNVs/CNAs outperforming all the other tools we compared. XCAVATOR is freely available at http://sourceforge.net/projects/xcavator/ .
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.