Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Sanger Sequencing

Sanger Sequencing

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...

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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....

RACE - Rapid Amplification of cDNA Ends

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

FALCON2: compression-based metagenomic classification of ancient viruses.

Bioinformatics (Oxford, England)·2026

Same author

An evaluation of computational methods for reconstruction of human viral DNA genomes.

GigaScience·2025

Same author

JARVIS3: an efficient encoder for genomic data.

Bioinformatics (Oxford, England)·2024

Same author

Machine Learning-Driven Discovery and Database of Cyanobacteria Bioactive Compounds: A Resource for Therapeutics and Bioremediation.

Journal of chemical information and modeling·2024

Same author

AltaiR: a C toolkit for alignment-free and temporal analysis of multi-FASTA data.

GigaScience·2024

Same author

Intra-host genomic diversity and integration landscape of human tissue-resident DNA virome.

Nucleic acids research·2024

Same journal

Feasibility of delivering a digital multiple health behaviour intervention via a home-telemonitoring system: engagement, outcomes, and user experiences.

BMC research notes·2026

Same journal

From manual entry to machine precision: challenges and evolution of metadata schema development in collaborative research centers.

BMC research notes·2026

Same journal

Sleep deprivation impairs gastric ulcer healing and induces anxiety-like behavior in rats.

BMC research notes·2026

Same journal

Caring across cultures: a qualitative exploration of Macedonian carers supporting community-dwelling older adults in a large regional city in Australia.

BMC research notes·2026

Same journal

Prevalence and determinants of dyslipidemia among residents of Kurdistan Region of Iraq; a community-based study.

BMC research notes·2026

Same journal

Modulation of brain-kidney crosstalk by olanzapine in aluminum chloride-induced memory impairment: a preclinical investigation.

BMC research notes·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 3, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

XS: a FASTQ read simulator.

Diogo Pratas¹, Armando J Pinho, João M O S Rodrigues

¹Signal Processing Lab, IEETA/DETI University of Aveiro, Aveiro 3810-193, Portugal. pratas@ua.pt.

BMC Research Notes

|January 18, 2014

Summary

This summary is machine-generated.

XS is a new FASTQ read simulator that generates realistic sequencing data without needing a reference genome. This flexible tool aids in testing bioinformatics pipelines and compression algorithms for next-generation sequencing (NGS).

More Related Videos

Author Spotlight: Cost-Effective Transcriptomic Drug Screening - Unlocking New Targets

Author Spotlight: Cost-Effective Transcriptomic Drug Screening - Unlocking New Targets

Published on: February 23, 2024

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms

Published on: February 2, 2024

Related Experiment Videos

Last Updated: May 3, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

Author Spotlight: Cost-Effective Transcriptomic Drug Screening - Unlocking New Targets

Author Spotlight: Cost-Effective Transcriptomic Drug Screening - Unlocking New Targets

Published on: February 23, 2024

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms

Published on: February 2, 2024

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Next-generation sequencing (NGS) generates massive data, necessitating specialized tools for analysis and infrastructure testing.
A need exists for flexible, portable FASTQ simulators that do not require a reference sequence for benchmarking.

Purpose of the Study:

To introduce XS, a versatile FASTQ read simulator designed for testing computational infrastructures and compression algorithms.
To provide a tool capable of generating realistic sequencing data with tunable complexity.

Main Methods:

XS simulates FASTQ files, including headers, DNA sequences, and quality scores, independently.
The simulator offers various running modes optimized for different time and memory constraints.
It is designed for portability and does not require a reference genome.

Main Results:

XS is a skilled, flexible, and portable FASTQ read simulation tool.
It allows for tunable sequence complexity and individual simulation of FASTQ components.
The tool supports multiple running modes for diverse computational environments.

Conclusions:

XS offers an efficient method for simulating FASTQ files from various sequencing platforms like Ion Torrent, Roche-454, Illumina, and ABI-SOLiD.
This simulator is particularly useful for testing cloud computing infrastructures and compression algorithms.
XS is publicly available for use in bioinformatics research.