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Related Concept Videos

Sanger Sequencing01:57

Sanger Sequencing

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...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

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Related Experiment Video

Updated: Jun 12, 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

SOPRA: Scaffolding algorithm for paired reads via statistical optimization.

Adel Dayarian1, Todd P Michael, Anirvan M Sengupta

  • 1Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey, USA.

BMC Bioinformatics
|June 26, 2010
PubMed
Summary
This summary is machine-generated.

SOPRA is a new tool that uses mate pair sequencing data to improve the assembly of short reads from high throughput sequencing (HTS) platforms. This method generates longer, high-quality scaffolds for bacterial genomes with minimal errors.

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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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Last Updated: Jun 12, 2026

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Published on: June 8, 2020

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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Published on: June 23, 2012

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • High throughput sequencing (HTS) generates vast amounts of short-read data, posing challenges for de novo genome assembly.
  • Mate pair technology offers a potential solution by providing paired reads with known distances.

Purpose of the Study:

  • To develop SOPRA, a novel tool for de novo genome assembly using mate pair and paired-end sequencing data.
  • To address the limitations of existing algorithms in handling short, error-prone HTS data.

Main Methods:

  • SOPRA models scaffold assembly as an optimization problem on a contig connectivity graph.
  • It iteratively refines the assembly by solving constraints and removing problematic contigs.
  • A dynamic programming approach is used for color-space to base-space translation on SOLiD data.

Main Results:

  • SOPRA successfully assembled bacterial genomes into long scaffolds (N50 up to 200 Kb).
  • The assembly process introduced very few errors, demonstrating high quality.
  • The tool effectively balances scaffold size and contiguity.

Conclusions:

  • SOPRA significantly improves scaffold assembly from mate pair sequencing data.
  • The methodology is applicable to various mate pair datasets for enhanced genome assembly.
  • This advancement aids in more accurate and comprehensive genome reconstruction.