ArticleScientific reports2011
Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions.
Article in Scientific reports, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 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
41 citing papers in PubMed.
- Biostatistical Aspects of Whole Genome Sequencing Studies: Preprocessing and Quality Control.Biometrical journal. Biometrische Zeitschrift · 2024Article
- Article
- Sequencing refractory regions in bird genomes are hotspots for accelerated protein evolution.BMC ecology and evolution · 2021Article
- Non-coding driver mutations in human cancer.Nature reviews. Cancer · 2021Review
- Application of Nanotechnology for Sensitive Detection of Low-Abundance Single-Nucleotide Variations in Genomic DNA: A Review.Nanomaterials (Basel, Switzerland) · 2021Review
- Evolutionary Constraint on Visual and Nonvisual Mammalian Opsins.Journal of biological rhythms · 2021Article
- Untargeted metagenomics shows a reliable performance for synchronous detection of parasites.Parasitology research · 2020Article
- ForestQC: Quality control on genetic variants from next-generation sequencing data using random forest.PLoS computational biology · 2019Article
- Similarities and differences between variants called with human reference genome HG19 or HG38.BMC bioinformatics · 2019Article
- Genome-Wide SNP Discovery in Indigenous Cattle Breeds of South Africa.Frontiers in genetics · 2019Article
- Genomic and Transcriptomic Characterization Links Cell Lines with Aggressive Head and Neck Cancers.Cell reports · 2018Article
- Cytogenetics and holoprosencephaly: A chromosomal microarray study of 222 individuals with holoprosencephaly.American journal of medical genetics. Part C, Seminars in medical genetics · 2018Article
- Mind the gap! The mitochondrial control region and its power as a phylogenetic marker in echinoids.BMC evolutionary biology · 2018Article
- Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms.Scientific reports · 2018Article
- IntroMap: a signal analysis based method for the detection of genomic introgressions.BMC genetics · 2017Article
- Article
- Characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data.Scientific reports · 2017Article
- Non-coding genetic variation in cancer.Current opinion in systems biology · 2017Article
- Comparative genetic analysis of the 45S rDNA intergenic spacers from three Saccharum species.PloS one · 2017Article
- Analysis of optimal alignments unfolds aligners' bias in existing variant profiles.BMC bioinformatics · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The rapid development of next generation sequencing (NGS) technology provides a new chance to extend the scale and resolution of genomic research. How to efficiently map millions of short reads to the reference genome and how to make accurate SNP calls are two major challenges in taking full advantage of NGS. In this article, we reviewed the current software tools for mapping and SNP calling, and evaluated their performance on samples from The Cancer Genome Atlas (TCGA) project. We found that BWA and Bowtie are better than the other alignment tools in comprehensive performance for Illumina platform, while NovoalignCS showed the best overall performance for SOLiD. Furthermore, we showed that next-generation sequencing platform has significantly lower coverage and poorer SNP-calling performance in the CpG islands, promoter and 5'-UTR regions of the genome. NGS experiments targeting for these regions should have higher sequencing depth than the normal genomic region.
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.