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Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.

Single Nucleotide Polymorphisms-SNPs

Single Nucleotide Polymorphisms-SNPs

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,...

Genomics

Genomics

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...

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Updated: May 8, 2026

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

NextGenMap: fast and accurate read mapping in highly polymorphic genomes.

Fritz J Sedlazeck¹, Philipp Rescheneder, Arndt von Haeseler

¹Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria and Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Waehringerstrasse 17, A-1090 Vienna, Austria.

Bioinformatics (Oxford, England)

|August 27, 2013

Summary

This summary is machine-generated.

NextGenMap is a novel read mapper that balances speed and accuracy, especially for highly polymorphic genomes. It offers superior performance and handles diverse sequencing data efficiently.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Read mapping is crucial for analyzing next-generation sequencing data.
Existing mappers often face a trade-off between mapping speed and accuracy in polymorphic regions.
Highly polymorphic genomes present significant challenges for accurate read alignment.

Purpose of the Study:

To introduce NextGenMap, a new read mapper designed to overcome the speed-accuracy trade-off.
To evaluate NextGenMap's performance against existing mapping tools.
To demonstrate NextGenMap's capability in handling diverse sequencing data and polymorphic genomes.

Main Methods:

NextGenMap utilizes multi-core CPUs and optionally GPUs for efficient hardware utilization.
The algorithm is designed to handle reads of varying lengths and from different sequencing technologies.
Performance was assessed based on runtime and the accuracy of mapped reads, particularly in challenging polymorphic regions.

Main Results:

NextGenMap achieves superior performance compared to current mapping methods in terms of both speed and accuracy.
It reliably aligns reads even with substantial sequence differences between the target and reference genomes.
The mapper demonstrates efficient use of computational resources, including multi-core CPUs and GPUs.

Conclusions:

NextGenMap effectively reduces the dilemma between speed and accuracy in read mapping.
It provides a robust solution for aligning sequencing reads to highly polymorphic genomes.
NextGenMap is a versatile tool capable of handling diverse sequencing data types and lengths automatically.