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

Sanger Sequencing01:57

Sanger Sequencing

772.5K
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...
772.5K
Lossy Lines and Overvoltages01:22

Lossy Lines and Overvoltages

316
Transmission-line series resistance and shunt conductance cause three primary effects: attenuation, distortion, and power losses.
Attenuation
When constant series resistance and shunt conductance are present, voltage and current equations are modified. The propagation constant indicates that voltage and current waves consist of both forward and backward traveling components. These waves attenuate as they propagate, with the attenuation factor related to the resistance and conductance. In a...
316
RNA-seq03:21

RNA-seq

11.6K
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...
11.6K
Downsampling01:20

Downsampling

552
When considering a sampled sequence with zero values between sampling instants, one can replace it by taking every N-th value of the sequence. At these integer multiples of N, the original and sampled sequences coincide. This process, known as decimation, involves extracting every N-th sample from a sequence, thereby creating a more efficient sequence.
The Fourier transform of the decimated sequence reveals a combination of scaled and shifted versions of the original spectrum. This...
552
Upsampling01:22

Upsampling

549
Managing signal sampling rates is essential in digital signal processing to maintain signal integrity. A decimated signal, characterized by a reduced frequency range due to its lower sampling rate, can be upsampled by inserting zeros between each sample. This upsampling process expands the original spectrum and introduces repeated spectral replicas at intervals dictated by the new Nyquist frequency. To refine this zero-inserted sequence, it is passed through a lowpass filter with a cutoff...
549
Next-generation Sequencing03:00

Next-generation Sequencing

97.4K
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....
97.4K

You might also read

Related Articles

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

Sort by
Same author

2022 IEEE conference on computational intelligence in bioinformatics and computational biology (IEEE CIBCB, 2022).

Bio Systems·2024
Same author

Freezing of gait in Parkinson's disease: Classification using computational intelligence.

Bio Systems·2023
Same author

All lockdowns are not equal: Reducing epidemic impact through evolutionary computation.

Bio Systems·2023
Same author

Effective decoders for DNA codes.

Bio Systems·2021
Same author

A centrality based multi-objective approach to disease gene association.

Bio Systems·2020
Same author

Models of Parkinson's Disease Patient Gait.

IEEE journal of biomedical and health informatics·2019

Related Experiment Video

Updated: Jan 1, 2026

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

12.6K

Lossy Compression of Quality Values in Sequencing Data.

Veronica Suaste Morales, Sheridan Houghten

    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    |December 24, 2019
    PubMed
    Summary

    Lossy compression techniques for DNA sequencing data, specifically SAM files, improve CRAM compression ratios. These methods do not harm, and may even enhance, single nucleotide polymorphism (SNP) calling accuracy.

    Area of Science:

    • Genomics
    • Bioinformatics
    • Data Compression

    Background:

    • The rapid expansion of human DNA sequencing generates vast amounts of data, creating significant storage challenges.
    • Compression techniques are crucial for managing large-scale genomic datasets, particularly SAM files used in DNA alignment.

    Purpose of the Study:

    • To investigate the effectiveness of lossy compression techniques for quality values in SAM files.
    • To analyze the impact of these lossy compression methods on the CRAM file format and single nucleotide polymorphism (SNP) calling.

    Main Methods:

    • Experiments were conducted using the NA12878 dataset with varying fold coverages.
    • A novel lossy compression model, dynamic binning, was introduced and compared against existing methods (Illumina binning, LEON, QVZ).

    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
    Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
    07:21

    Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

    Published on: August 25, 2018

    13.3K

    Related Experiment Videos

    Last Updated: Jan 1, 2026

    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

    12.6K
    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
    Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
    07:21

    Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

    Published on: August 25, 2018

    13.3K
  • Compression ratios for CRAM files and SNP calling performance were evaluated.

    • Main Results:

    • Lossy compression techniques significantly improve the compression ratio of CRAM files.
    • The evaluated lossy techniques did not negatively impact SNP calling accuracy.
    • In some instances, lossy compression even demonstrated a potential to boost SNP calling performance.

    Conclusions:

    • Lossy compression is a viable strategy for reducing the storage footprint of genomic data in CRAM format.
    • The application of lossy compression for quality values in SAM files offers benefits without compromising essential downstream analyses like SNP calling.