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NSIT: novel sequence identification tool.

Benjarath Pupacdi1, Asif Javed2, Mohammed J Zaki3

  • 1Translational Research Unit, Chulabhorn Research Institute, Bangkok, Thailand.

Plos One
|September 30, 2014
PubMed
Summary

A new tool, NSIT, accurately identifies novel DNA sequences in individual genomes. This software helps uncover unique genetic variations and potential contamination, improving de novo genome assembly analysis.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Novel DNA sequences are unique to an individual and absent in the human reference genome.
  • These sequences are important for understanding human diversity and migration patterns.
  • Existing methods for identifying novel sequences in de novo assemblies are insufficient.

Purpose of the Study:

  • To develop a specialized computational tool for accurate and efficient identification of novel sequences in de novo genome assemblies.
  • To characterize novel sequences in diverse human genomes.
  • To assess the potential for sequence contamination in genome assemblies.

Main Methods:

  • Development of the Novel Sequence Identification Tool (NSIT).
  • Application of NSIT to de novo whole genome assemblies of NA18507 (African), YH (Asian), and NA12878 (European).
  • Development of a graphical viewer for comparing novel sequence content and identifying contamination.

Main Results:

  • NSIT accurately identified 1.0-1.2 Mb of novel sequences in the tested individuals.
  • Results suggest the total amount of novel sequences per individual might be lower than previously estimated.
  • Identified sequence contamination, including Epstein-Barr virus and zebrafish repeats, in previously published data.
  • NSIT is efficient, requiring minimal RAM and running in 1.5-2 hours on standard hardware.
  • The tool supports various assembly sizes and system architectures.

Conclusions:

  • NSIT is the first dedicated software for novel sequence identification in de novo human genome assemblies.
  • The tool provides accurate and efficient analysis, aiding in the discovery of individual-specific genomic variations.
  • NSIT's ability to detect contamination enhances the reliability of genome assembly analysis.