BRCA-analyzer: Automatic workflow for processing NGS reads of BRCA1 and BRCA2 genes
Sign Up to like & getrecommendations! Published in 2018 at "Computational biology and chemistry"
DOI: 10.1016/j.compbiolchem.2018.10.012
Abstract: The use of targeted next-generation sequencing (NGS) provides great new opportunities for molecular and medical genetics. However, in order to take advantage of these opportunities, we need to have reliable tools for extracting the necessary… read more here.
Keywords: brca analyzer; processing ngs; analyzer; workflow processing ... See more keywords
Detecting viral sequences in NGS data.
Sign Up to like & getrecommendations! Published in 2019 at "Current opinion in virology"
DOI: 10.1016/j.coviro.2019.07.010
Abstract: Next generation sequencing (NGS) technologies provide an increasingly important avenue for detecting known viruses, and for discovering novel viruses present in clinical or environmental samples. Several computational pipelines capable of identifying and classifying viral sequences… read more here.
Keywords: detecting viral; virology; sequences ngs; ngs data ... See more keywords
Computational analysis of next generation sequencing data and its applications in clinical oncology
Sign Up to like & getrecommendations! Published in 2018 at "Informatics in Medicine Unlocked"
DOI: 10.1016/j.imu.2018.05.003
Abstract: Abstract Next generation sequencing (NGS) has made great strides in sequencing technology as it enables sequencing of genes in a high throughput manner with low cost. Various NGS platforms such as Illumina, Roche, ABI/SOLiD are… read more here.
Keywords: analysis; clinical oncology; next generation; ngs data ... See more keywords
Detecting sample swaps in diverse NGS data types using linkage disequilibrium
Sign Up to like & getrecommendations! Published in 2020 at "Nature Communications"
DOI: 10.1038/s41467-020-17453-5
Abstract: As the number of genomics datasets grows rapidly, sample mislabeling has become a high stakes issue. We present CrosscheckFingerprints (Crosscheck), a tool for quantifying sample-relatedness and detecting incorrectly paired sequencing datasets from different donors. Crosscheck… read more here.
Keywords: sample; ngs data; swaps diverse; diverse ngs ... See more keywords
Bio-Docklets: virtualization containers for single-step execution of NGS pipelines
Sign Up to like & getrecommendations! Published in 2017 at "GigaScience"
DOI: 10.1093/gigascience/gix048
Abstract: Abstract Processing of next-generation sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution of bioinformatics data pipelines, in addition to specialized postanalysis visualization and data mining software. In order to address some… read more here.
Keywords: virtualization containers; containers single; ngs data; execution ... See more keywords
1210. K-mer Profiling Powered by Reference-assisted Assembly of NGS Data: A Highly Sensitive Protocol to Infer the Plasma Microbiome Using Cell-free DNA Sequence Data
Sign Up to like & getrecommendations! Published in 2020 at "Open Forum Infectious Diseases"
DOI: 10.1093/ofid/ofaa439.1395
Abstract: Cell-free DNA (cfDNA) has emerged as an important clinical specimen to probe for pathogenic microbes, especially in organ transplant patients where the same data can be used to predict allograft rejection. Recent reports described viral,… read more here.
Keywords: reference assisted; dna; assisted assembly; protocol ... See more keywords
GANDAFL: Dataflow Acceleration for Short Read Alignment on NGS Data
Sign Up to like & getrecommendations! Published in 2022 at "IEEE Transactions on Computers"
DOI: 10.1109/tc.2022.3144115
Abstract: DNA read alignment is an integral part of genome study, which has been revolutionised thanks to the growth of Next Generation Sequencing (NGS) technologies. The inherent computational intensity of string matching algorithms such as Smith-Waterman… read more here.
Keywords: short read; ngs data; acceleration; read alignment ... See more keywords
Next-Generation Sequencing Markup Language (NGSML): A Medium for the Representation and Exchange of NGS Data
Sign Up to like & getrecommendations! Published in 2022 at "IEEE/ACM Transactions on Computational Biology and Bioinformatics"
DOI: 10.1109/tcbb.2022.3144170
Abstract: With the increasing demand for low-cost high-throughput sequencing of large genomes, next-generation sequencing (NGS) technology has developed rapidly. NGS can not only be used in basic scientific research but also in clinical diagnostics and healthcare.… read more here.
Keywords: ngs data; markup language; language ngsml; representation exchange ... See more keywords
Screening for prevalence and abundance of Capnocytophaga spp by analyzing NGS data. A scoping review.
Sign Up to like & getrecommendations! Published in 2020 at "Oral diseases"
DOI: 10.1111/odi.13573
Abstract: BACKGROUND Capnocytophaga spp. are commensal bacteria of the oral cavity and constitute a genus of the core microbiome. OBJECTIVE This genus is responsible for many local and systemic conditions in both the immunocompetent and immunocompromised,… read more here.
Keywords: capnocytophaga spp; capnocytophaga; abundance capnocytophaga; ngs data ... See more keywords
An Easy-to-Use Approach to Detect CNV From Targeted NGS Data: Identification of a Novel Pathogenic Variant in MO Disease
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Endocrinology"
DOI: 10.3389/fendo.2022.874126
Abstract: Background Despite the new next-generation sequencing (NGS) molecular approaches implemented the genetic testing in clinical diagnosis, copy number variation (CNV) detection from NGS data remains difficult mainly in the absence of bioinformatics personnel (not always… read more here.
Keywords: easy use; ngs data; detection; use approach ... See more keywords
Bioinformatics: From NGS Data to Biological Complexity in Variant Detection and Oncological Clinical Practice
Sign Up to like & getrecommendations! Published in 2022 at "Biomedicines"
DOI: 10.3390/biomedicines10092074
Abstract: The use of next-generation sequencing (NGS) techniques for variant detection has become increasingly important in clinical research and in clinical practice in oncology. Many cancer patients are currently being treated in clinical practice or in… read more here.
Keywords: bioinformatics ngs; clinical practice; variant detection; ngs data ... See more keywords