Related Experiment Video
Updated: Dec 28, 2025
13:33
Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
39.7K
Metagenome SNP calling via read-colored de Bruijn graphs
Bahar Alipanahi1, Martin D Muggli1, Musa Jundi1
1Department of Computer & Information Science & Engineering, University of Florida, Gainesville, FL 32611, USA.
Bioinformatics (Oxford, England)
|February 13, 2020
Summary
LueVari is a novel, reference-free tool for accurately identifying single-nucleotide polymorphisms (SNPs) in metagenomic data. This advancement aids in tracking microbial organisms and antimicrobial resistance genes without needing reference genomes.
Area of Science:
- Genomics
- Bioinformatics
- Microbiology
Background:
- Metagenomics studies microbial communities and antimicrobial resistance (AMR) genes.
- Single-nucleotide polymorphisms (SNPs) are crucial for tracking organisms and genes.
- Current SNP callers require reference genomes, which are often unavailable for unculturable microbes.
Purpose of the Study:
- To develop a scalable and accurate metagenomics SNP caller.
- To create a tool that does not rely on reference genomes.
- To enable effective traceability of organisms and AMR genes in complex samples.
Main Methods:
- Developed LueVari, a reference-free SNP caller.
- Utilized a read-colored de Bruijn graph for unambiguous identification of variations.
- Applied the caller to shotgun metagenomics data.
Main Results:
- LueVari achieves high sensitivity (91–99%) and precision (71–99%) in identifying SNPs.
- The tool accurately identifies SNPs in both AMR genes and chromosomal DNA.
- LueVari constructs variation-spanning sequences, covering up to 97.8% of genes.
Conclusions:
- LueVari provides a robust solution for SNP detection in metagenomics without reference genomes.
- The tool enhances the ability to trace microbial populations and AMR gene dynamics.
- LueVari is a valuable asset for microbiome and resistome research.
Related Concept Videos
02:26Comparing Copy Number Variations and SNPs
18.5K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
18.5K
01:11Genome-wide Association Studies-GWAS
15.2K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
15.2K
01:05Single Nucleotide Polymorphisms-SNPs
17.8K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
17.8K
01:57Sanger Sequencing
772.3K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
772.3K
02:02Genomics
39.5K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
39.5K
03:36Genome Annotation and Assembly
20.4K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
20.4K