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

COPD: Pathogenesis and Clinical Features01:20

COPD: Pathogenesis and Clinical Features

1.8K
Chronic obstructive pulmonary disease (COPD) is a group of lung conditions that progressively worsen over time, including chronic bronchitis and emphysema. This cluster of diseases collectively leads to a gradual and irreversible decline in lung function over time.
The primary cause for the onset of COPD is cigarette smoking and exposure to air pollution. These hazardous factors initiate a chain reaction within the lungs, resulting in chronic inflammation, damage to the airways, and a...
1.8K
Special Features of Adaptive Immunity01:20

Special Features of Adaptive Immunity

3.3K
The adaptive immune system, a crucial component of the overall immune response, offers a highly specialized defense against pathogens. It involves specific cell types and features, enabling it to combat infections effectively and efficiently.
The primary cell types involved in adaptive immunity are T cells and B cells. Each type has a unique role in defending the body against pathogens. T cells are responsible for cell-mediated immunity. They identify and eliminate infected cells directly,...
3.3K
Esophageal Strictures-II: Clinical Features and Management01:26

Esophageal Strictures-II: Clinical Features and Management

632
Patients with esophageal strictures often experience a range of symptoms. Initially, they may have difficulty swallowing solid foods, which can progress to include liquids. Additional symptoms may involve chest pain or discomfort, regurgitating food and fluids, heartburn, unintentional weight loss, coughing or choking during meals, and hoarseness.
Healthcare providers should gather a comprehensive medical history and conduct a physical examination for diagnosis. If esophageal stricture is...
632
Endocarditis II: Clinical Features of Infective Endocarditis01:25

Endocarditis II: Clinical Features of Infective Endocarditis

514
Endocarditis can present various clinical features depending on the causative organism and the patient's underlying health conditions. Initially, the clinical features of infective endocarditis develop gradually, presenting with nonspecific symptoms that can be easily mistaken for other illnesses.General SymptomsEarly symptoms of infective endocarditis are fever, chills, weakness, malaise, fatigue, and weight loss. These symptoms reflect the systemic nature of the infection and the body's...
514
Pericarditis II: Clinical Features and Diagnostic Tests01:19

Pericarditis II: Clinical Features and Diagnostic Tests

329
Pericarditis is distinguished by inflammation of the pericardium, the fibrous sac that encases the heart. It can be acute, lasting less than six weeks, or chronic, persisting for over three months. Understanding its clinical manifestations and diagnostic findings is crucial for timely and effective management.Clinical ManifestationsWhile pericarditis can be asymptomatic, it usually presents with characteristic symptoms such as:Chest Pain: The most characteristic symptom of pericarditis is chest...
329
Esophageal Varices-II: Clinical Features and Management01:28

Esophageal Varices-II: Clinical Features and Management

573
Esophageal varices often manifest as gastrointestinal bleeding episodes, presenting symptoms like hematemesis (vomiting of blood), hematochezia (passing fresh blood via the rectum), and melena (black, tarry stools). Other signs can include weight loss, anorexia, abdominal discomfort, jaundice, pruritus, altered mental status, and muscle cramps.
In the initial assessment, a thorough review of the patient's medical history is vital to identify risk factors such as liver disease, alcohol...
573

You might also read

Related Articles

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

Sort by
Same author

HOROSCOPE: Decoding human centromere architecture from short reads using <i>k</i>-mer signatures.

bioRxiv : the preprint server for biology·2026
Same author

Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures.

bioRxiv : the preprint server for biology·2026
Same author

GEAR Genomics: a user-friendly, open-source web platform enabling interactive genomic analysis for molecular biologists.

Nucleic acids research·2026
Same author

Recurrent DNA break clusters drive replication-stress-induced copy number variants and genome diversification.

Nature communications·2026
Same author

Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion.

Nature communications·2026
Same author

Leveraging a spectrum of cytogenomics methods for profiling complex karyotypes in chronic lymphocytic leukemia.

Human genomics·2026

Related Experiment Video

Updated: Feb 1, 2026

Amplicon Sequencing using the Long-Read Sequencing Technologies
08:57

Amplicon Sequencing using the Long-Read Sequencing Technologies

Published on: August 29, 2025

532

Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and

Tobias Rausch1,2, Markus Hsi-Yang Fritz2, Jan O Korbel2

  • 1Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, Germany.

Bioinformatics (Oxford, England)
|December 7, 2018
PubMed
Summary

Alfred is a new command-line tool for harmonizing quality control of large-scale sequencing data. It provides multi-sample QC metrics and supports advanced analyses for various sequencing technologies.

More Related Videos

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

5.8K
Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

12.8K

Related Experiment Videos

Last Updated: Feb 1, 2026

Amplicon Sequencing using the Long-Read Sequencing Technologies
08:57

Amplicon Sequencing using the Long-Read Sequencing Technologies

Published on: August 29, 2025

532
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

5.8K
Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

12.8K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Harmonizing quality control (QC) for large-scale second and third-generation sequencing data is crucial for downstream analyses.
  • Existing QC methods may lack versatility across diverse sequencing assays and technologies.

Purpose of the Study:

  • To present Alfred, an efficient and versatile command-line application for multi-sample QC of sequencing data.
  • To enable read-group aware metric computation across various sequencing assays and technologies.

Main Methods:

  • Developed Alfred, a command-line application for calculating QC metrics.
  • Implemented support for standard QC metrics (GC bias, base composition, insert size, coverage).
  • Integrated haplotype-aware and allele-specific feature counting and annotation capabilities.
  • Included haplo-tagging for haplotype-resolved analyses of BAM/CRAM files.

Main Results:

  • Alfred computes multi-sample QC metrics in a read-group aware manner.
  • The tool supports a wide variety of sequencing assays and technologies.
  • It facilitates easy pipeline integration for high-throughput settings and large-scale initiatives.
  • A companion web application allows interactive exploration and comparison of results.

Conclusions:

  • Alfred provides a versatile solution for continuous monitoring of sequence data quality.
  • The application supports advanced haplotype-resolved analyses.
  • Alfred is open-source and freely available, promoting wider adoption in genomics research.