Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations
Mutations, the fuel of evolution, are first manifested as rare DNA changes within a population
of cells. Although next-generation sequencing (NGS) technologies have revolutionized the …
of cells. Although next-generation sequencing (NGS) technologies have revolutionized the …
Sequencing pools of individuals—mining genome-wide polymorphism data without big funding
The analysis of polymorphism data is becoming increasingly important as a complementary
tool to classical genetic analyses. Nevertheless, despite plunging sequencing costs …
tool to classical genetic analyses. Nevertheless, despite plunging sequencing costs …
LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets
The study of cell-population heterogeneity in a range of biological systems, from viruses to
bacterial isolates to tumor samples, has been transformed by recent advances in …
bacterial isolates to tumor samples, has been transformed by recent advances in …
[HTML][HTML] A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data
C Xu - Computational and structural biotechnology journal, 2018 - Elsevier
Detection of somatic mutations holds great potential in cancer treatment and has been a
very active research field in the past few years, especially since the breakthrough of the next …
very active research field in the past few years, especially since the breakthrough of the next …
A survey of tools for variant analysis of next-generation genome sequencing data
S Pabinger, A Dander, M Fischer… - Briefings in …, 2014 - academic.oup.com
Recent advances in genome sequencing technologies provide unprecedented opportunities
to characterize individual genomic landscapes and identify mutations relevant for diagnosis …
to characterize individual genomic landscapes and identify mutations relevant for diagnosis …
SNP discovery through next-generation sequencing and its applications
S Kumar, TW Banks, S Cloutier - Crop Breeding, 2016 - taylorfrancis.com
Molecular markers are widely used in plant genetic research and breeding. Single
Nucleotide Polymorphisms (SNPs) are currently the marker of choice due to their large …
Nucleotide Polymorphisms (SNPs) are currently the marker of choice due to their large …
Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing
Background To facilitate the clinical implementation of genomic medicine by next-generation
sequencing, it will be critically important to obtain accurate and consistent variant calls on …
sequencing, it will be critically important to obtain accurate and consistent variant calls on …
Evaluating variant calling tools for non-matched next-generation sequencing data
S Sandmann, AO De Graaf, M Karimi… - Scientific reports, 2017 - nature.com
Valid variant calling results are crucial for the use of next-generation sequencing in clinical
routine. However, there are numerous variant calling tools that usually differ in algorithms …
routine. However, there are numerous variant calling tools that usually differ in algorithms …
Genomic prediction in maize breeding populations with genotyping-by-sequencing
Abstract Genotyping-by-sequencing (GBS) technologies have proven capacity for delivering
large numbers of marker genotypes with potentially less ascertainment bias than standard …
large numbers of marker genotypes with potentially less ascertainment bias than standard …
INDEL detection, the 'Achilles heel'of precise genome editing: a survey of methods for accurate profiling of gene editing induced indels
EP Bennett, BL Petersen, IE Johansen… - Nucleic acids …, 2020 - academic.oup.com
Advances in genome editing technologies have enabled manipulation of genomes at the
single base level. These technologies are based on programmable nucleases (PNs) that …
single base level. These technologies are based on programmable nucleases (PNs) that …