Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Video

Updated: May 10, 2026

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
06:40

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner.

Ruibang Luo1, Thomas Wong, Jianqiao Zhu

  • 1HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, China.

Plos One
|June 7, 2013
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

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

Sort by
Same author

Ultrasound-Recharged Sub-Nanometer Palladium Catalysts for on-Demand and Self-Terminating Bioorthogonal Prodrug Activation in Cancer Therapy.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026
Same author

An Adaptive Ionic Sieve: Flexible Hydrogen-Bonded Organic Frameworks Decouple the Trade-Off Between Zn Ions Desolvation and Mass Transfer.

Angewandte Chemie (International ed. in English)·2026
Same author

Efficient one-pot lactic acid production from cellulose via a Trichoderma reesei and Bacillus coagulans cooperation leveraging substrate-induced secretomes.

Bioresource technology·2026
Same author

Unexpected Bilateral Lacrimal and Salivary Gland Uptake of 68Ga-DOTA-Ibandronic Acid on PET/CT.

Clinical nuclear medicine·2026
Same author

Insufficient ferroptosis in radiation-induced tumor cells promote Treg cell generation to induce radiotherapy resistance.

Communications biology·2026
Same author

Advances in PD-L1 Targeted Molecular Imaging Radiotracers Research: From Preclinical Exploration to Clinical Application.

Molecular imaging and biology·2026
Same journal

Analysis of strength degradation of coal and rock masses and stability of mined areas under long term immersion environment.

PloS one·2026
Same journal

Biogenic Silver-Selenium nanocomposite with anticancer activity and potent efficacy against vancomycin-resistant Staphylococcus aureus.

PloS one·2026
Same journal

Preparation and physicochemical characterization of a biodegradable chitosan/carboxymethyl cellulose hydrogel synthesized in NaOH/urea medium.

PloS one·2026
Same journal

Action-guilt, survivor-guilt, and depression in combat-related PTSD.

PloS one·2026
Same journal

Explainable machine learning for predicting activities of daily living at discharge in stroke patients: A retrospective study using SHAP interpretability.

PloS one·2026
Same journal

Deep learning based two-way feature depiction model for brain tumor detection.

PloS one·2026
See all related articles

SOAP3-dp is a novel Next-Generation Sequencing (NGS) aligner that achieves high speed and sensitivity simultaneously. It outperforms existing aligners, enabling more accurate variant and indel discovery with a low false discovery rate (FDR).

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Next-Generation Sequencing (NGS) generates vast amounts of data, necessitating efficient and accurate short-read alignment.
  • Existing aligners often trade accuracy for speed, limiting comprehensive genomic analysis.

Purpose of the Study:

  • To develop and evaluate SOAP3-dp, a high-performance short-read aligner.
  • To demonstrate SOAP3-dp's ability to achieve both high speed and high sensitivity simultaneously for NGS data.

Main Methods:

  • SOAP3-dp leverages both CPU and GPU computational power with optimized algorithms.
  • It tolerates low alignment similarity (down to 60%) and supports gapped alignments.
  • Evaluated against widely adopted aligners including BWA, Bowtie2, and GPU-based aligners.

More Related Videos

Online Size-exclusion and Ion-exchange Chromatography on a SAXS Beamline
11:09

Online Size-exclusion and Ion-exchange Chromatography on a SAXS Beamline

Published on: January 5, 2017

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Related Experiment Videos

Last Updated: May 10, 2026

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
06:40

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

Online Size-exclusion and Ion-exchange Chromatography on a SAXS Beamline
11:09

Online Size-exclusion and Ion-exchange Chromatography on a SAXS Beamline

Published on: January 5, 2017

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Main Results:

  • SOAP3-dp is two to tens of times faster than existing aligners while maintaining superior sensitivity and the lowest false discovery rate (FDR).
  • Demonstrated enhanced discovery of authentic variants and longer insertions/deletions (Indels) in human genome data.
  • Achieved a 9.1% FDR on newly discovered deletions using fosmid sequencing.

Conclusions:

  • SOAP3-dp offers a significant advancement in short-read alignment for NGS data.
  • Its performance enables more accurate and sensitive variant detection, facilitating deeper genomic insights.
  • Native BAM support and BWA compatibility ensure seamless integration into existing bioinformatics pipelines.