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 Concept Videos

You might also read

Related Articles

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

Sort by
Same author

Privacy-Enhanced Vertical Federated Learning for Healthcare via Directional Noise and Subset Representations.

IEEE journal of biomedical and health informatics·2026
Same author

Selection of proper artificial intelligence techniques developed for CT scan image analysis of liver cancer using fuzzy AHP-TOPSIS.

BMC medical imaging·2026
Same author

Identification and functional characterization of a novel mutation in the NEUROD1 gene in a Chinese family with maturity-onset diabetes of the young.

Acta diabetologica·2026
Same author

MFDA-UNet: Medical Image Segmentation with Frequency-Decoupled Representation and Gated Cross-Scale Integration.

Sensors (Basel, Switzerland)·2026
Same author

Analysis of Long-Term and Short-Term Efficacy of Different Types of Tympanosclerosis Surgery Under Total Otoendoscopy.

The Annals of otology, rhinology, and laryngology·2026
Same author

MiR-26b-5p Predicts the Severity of Crohn's Disease and the Degree of Malnutrition.

Folia biologica·2026
Same journal

CNV-ECOD: A copy number variation detection method based on ECOD algorithm using next-generation sequencing data.

Journal of bioinformatics and computational biology·2026
Same journal

ReinVar: A model-free paradigm-based reinforcement learning approach to detect copy number variation.

Journal of bioinformatics and computational biology·2026
Same journal

When pipelines run but coordinates fail: A simple spatial specificity check for false locality in post-GWAS analysis.

Journal of bioinformatics and computational biology·2026
Same journal

Comparative benchmarking of template-based, evolutionary-diffusion, and generative language models for IsPETase structure prediction.

Journal of bioinformatics and computational biology·2026
Same journal

Trap spaces as labelled ideals of SCC posets: A structural-functional theory of reachability in asynchronous boolean networks.

Journal of bioinformatics and computational biology·2026
Same journal

Erratum - DDINet: Drug-drug interaction prediction network based on multi-molecular fingerprint features and multi-head attention centered weighted autoencoder.

Journal of bioinformatics and computational biology·2026
See all related articles

Related Experiment Video

Updated: Dec 29, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

5.7K

AUSPP: A universal short-read pre-processing package.

Lei Gao1, Cong Wu1, Lin Liu1

  • 1The Key Laboratory of Plant Epigenetics of Guangdong Province, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China.

Journal of Bioinformatics and Computational Biology
|February 6, 2020
PubMed
Summary
This summary is machine-generated.

AUSPP is a versatile pipeline that automates the pre-processing of next-generation sequencing (NGS) short reads and their mapping to reference genomes. This tool simplifies complex bioinformatics workflows, making NGS data analysis more accessible.

Keywords:
Next-generation sequencing (NGS)Perl scriptpipelinepre-processingshort reads

More Related Videos

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

3.8K
A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells
06:02

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

Published on: October 28, 2025

340

Related Experiment Videos

Last Updated: Dec 29, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

5.7K
Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

3.8K
A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells
06:02

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

Published on: October 28, 2025

340

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Next-generation sequencing (NGS) generates vast amounts of short-read data that require extensive pre-processing before analysis.
  • Existing tools often lack specialization in handling diverse NGS data types and integrating pre-processing with mapping.
  • Efficient pre-processing is crucial for accurate downstream analyses, including meta-analysis.

Purpose of the Study:

  • To present AUSPP, a Perl script-based pipeline for the automated pre-processing and mapping of NGS short reads.
  • To provide a comprehensive solution that streamlines the workflow from raw sequencing data to genome mapping.
  • To offer a user-friendly tool with default settings for various NGS data types, simplifying the analysis process.

Main Methods:

  • Development of a Perl script-based pipeline named AUSPP.
  • Integration of multiple pre-processing steps: quality control, adaptor trimming, read collapsing, structural RNA removal, and length selection.
  • Implementation of automatic read mapping to a reference genome and normalized wiggle file creation.

Main Results:

  • AUSPP successfully integrates quality control, adaptor trimming, and read mapping into a single pipeline.
  • The pipeline automates the creation of normalized wiggle files, essential for visualization and further analysis.
  • Default settings enable efficient processing for many NGS data types, requiring minimal user input.

Conclusions:

  • AUSPP significantly simplifies and accelerates the pre-processing and mapping of NGS short reads.
  • The pipeline serves as a powerful tool for researchers preparing data for meta-analysis.
  • AUSPP is portable, easy to install, and freely available, promoting wider adoption in the scientific community.