• HOME
  • NEWS
    • BIOENGINEERING
    • SCIENCE NEWS
  • EXPLORE
    • CAREER
      • Companies
      • Jobs
    • EVENTS
    • iGEM
      • News
      • Team
    • PHOTOS
    • VIDEO
    • WIKI
  • BLOG
  • COMMUNITY
    • FACEBOOK
    • FORUM
    • INSTAGRAM
    • TWITTER
  • CONTACT US
Wednesday, June 29, 2022
BIOENGINEER.ORG
No Result
View All Result
  • Login
  • HOME
  • NEWS
    • BIOENGINEERING
    • SCIENCE NEWS
  • EXPLORE
    • CAREER
      • Companies
      • Jobs
        • Lecturer
        • PhD Studentship
        • Postdoc
        • Research Assistant
    • EVENTS
    • iGEM
      • News
      • Team
    • PHOTOS
    • VIDEO
    • WIKI
  • BLOG
  • COMMUNITY
    • FACEBOOK
    • FORUM
    • INSTAGRAM
    • TWITTER
  • CONTACT US
  • HOME
  • NEWS
    • BIOENGINEERING
    • SCIENCE NEWS
  • EXPLORE
    • CAREER
      • Companies
      • Jobs
        • Lecturer
        • PhD Studentship
        • Postdoc
        • Research Assistant
    • EVENTS
    • iGEM
      • News
      • Team
    • PHOTOS
    • VIDEO
    • WIKI
  • BLOG
  • COMMUNITY
    • FACEBOOK
    • FORUM
    • INSTAGRAM
    • TWITTER
  • CONTACT US
No Result
View All Result
Bioengineer.org
No Result
View All Result
Home NEWS Science News

Rapid validation for genome assemblies? Introducing KAT: K-mer Analysis Toolkit

Bioengineer by Bioengineer
December 5, 2016
in Science News
0
Share on FacebookShare on TwitterShare on LinkedinShare on RedditShare on Telegram

Genome assembly projects are costly in both time and money; where identifying problems with your data post-assembly can be a real setback. With the K-mer Analysis Toolkit (KAT), researchers can access and confirm their results at every stage.

Genome assembly with NGS technologies is like trying to do the hardest jigsaw puzzle you can imagine. The final jigsaw represents the full genome, and the individual pieces represent small fragments of the genome read out by the sequencer. Counterintuitively, to make the data more manageable, it is actually easier to first break these pieces into even smaller pieces called K-mers.

K-mers represent small fragments of the original genome with a fixed number (K) of DNA base pairs. A computer can efficiently work with large quantities of K-mers, then identify connections between these fragments to build-up a representation of the original genome.

K-mer-based techniques are commonly used to efficiently generate genome assemblies, KAT, however, is built to examine and compare K-mer datasets, using each distinct K-mer's underlying properties, such as frequency and nucleotide composition.

Initially, KAT can analyse sequencing data to identify error levels, biases and contamination. Information from this analysis can help researchers decide whether to proceed with downstream tasks such as genome assembly. KAT can then internally back-check your assembly to determine completeness and accuracy without any external reference data – a really useful feature when studying new organisms.

Lead Software Developer, Daniel Mapleson, said on the new tool: "Imagine genome assembly like lego. Instead of trying to piece together long, 8×2-stud pieces with 6×2-stud pieces and 5×2-stud pieces, it's more like making a staircase pattern out of the smaller 2×2-bit pieces, overlapping one stud at a time.

"However, K-mers are not only useful for assembling a genome, by counting the number of K-mers in a sequencing dataset you can learn a lot about it. By looking at the K-mer frequency profiles (K-mer spectra) we can assess the quality of the sequencing data in the first instance, such as working out if the dataset is clean, contains contaminants or is biased in some way. KAT can give answers to these questions quickly, even for non-model organisms where a reference is not available."

Project Leader and corresponding author Bernardo Clavijo commented: "The first thing many researchers do after sequencing a genome is to use-check the K-mer spectra of their data. This tells you if the information you will need to assemble the genome is there before you spend a lot of time, effort and money on doing the rest of the analysis. Now with KAT, researchers can do all kinds of validation and information comparison at this initial stage; but to also carry this forward to validation, we have included the relevant information at the end of the assembly.

"In terms of assembly validation, the tool is particularly useful with diploid genomes that can carry more than one copy of a gene, certain regions can be falsely duplicated or deleted during assembly, leading the researcher to believe there's more or less copies of a gene than there really are. KAT can help to detect these artefacts by tracking both the data generated from the sequencer and data from the assembler, ultimately leading to faster, more accurate conclusions."

###

The paper titled: KAT: A K-mer Analysis Toolkit to quality control NGS datasets and genome assemblies is published in Bioinformatics.

For more information, read our article: KAT got your tongue? An analysis tool to quickly detect problems in sequencing data and genome assemblies.

Media Contact

Hayley London
[email protected]
160-345-0107

http://www.earlham.ac.uk/

############

Story Source: Materials provided by Scienmag

Share12Tweet7Share2ShareShareShare1

Related Posts

Group Leader in Chemical Proteomics, Dr. Guillaume Médard, and his research group in the lab.

Shining some light on the obscure proteome

June 29, 2022
Matthew Goldberg, Associate Research Scientist, Yale Program on Climate Change Communication

Romantic partners can influence each other’s beliefs and behaviors on climate change, new Yale study finds

June 29, 2022

The world’s rivers are changing, here’s how

June 29, 2022

Immune cells anchored in tissues offer unique defenses against pathogens and cancers

June 29, 2022
Please login to join discussion

POPULAR NEWS

  • Pacific whiting

    Oregon State University research finds evidence to suggest Pacific whiting skin has anti-aging properties that prevent wrinkles

    37 shares
    Share 15 Tweet 9
  • University of Miami Rosenstiel School selected for National ‘Reefense’ Initiative focusing on Florida and the Caribbean

    35 shares
    Share 14 Tweet 9
  • Saving the Mekong delta from drowning

    37 shares
    Share 15 Tweet 9
  • Sharks may be closer to the city than you think, new study finds

    34 shares
    Share 14 Tweet 9

About

We bring you the latest biotechnology news from best research centers and universities around the world. Check our website.

Follow us

Tags

VirologyViolence/CriminalsZoology/Veterinary ScienceUniversity of WashingtonWeather/StormsUrbanizationVaccineUrogenital SystemVirusVaccinesVehiclesWeaponry

Recent Posts

  • Shining some light on the obscure proteome
  • Romantic partners can influence each other’s beliefs and behaviors on climate change, new Yale study finds
  • The world’s rivers are changing, here’s how
  • Immune cells anchored in tissues offer unique defenses against pathogens and cancers
  • Contact Us

© 2019 Bioengineer.org - Biotechnology news by Science Magazine - Scienmag.

No Result
View All Result
  • Homepages
    • Home Page 1
    • Home Page 2
  • News
  • National
  • Business
  • Health
  • Lifestyle
  • Science

© 2019 Bioengineer.org - Biotechnology news by Science Magazine - Scienmag.

Welcome Back!

Login to your account below

Forgotten Password?

Retrieve your password

Please enter your username or email address to reset your password.

Log In
Posting....