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Related Concept Videos

Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Genome-wide Association Studies-GWAS01:11

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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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. 
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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Related Experiment Video

Updated: Mar 21, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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SwarmGenomics: A Unified Pipeline for Individual-Based Whole-Genome Analyses.

Aure Kylmänen1, Yu-Chi Chen1, Sahar Javaheri Tehrani1

  • 1Computational Systems Biology, Faculty of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany.

Molecular Ecology Resources
|March 19, 2026
PubMed
Summary

SwarmGenomics is a user-friendly pipeline simplifying whole-genome sequencing (WGS) analysis for non-model species. It provides essential tools for genetic diversity and population history insights, making complex genomic research more accessible.

Keywords:
NUMTPSMCbioinformatics pipelineheterozygositymitochondrial genomerepeat annotationruns of homozygosityunmapped readswhole‐genome sequencing

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Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Whole-genome sequencing (WGS) data is increasingly accessible but challenging to analyze.
  • Existing WGS analysis requires specialized tools and significant bioinformatics expertise.
  • Non-model species often lack dedicated genomic analysis pipelines.

Purpose of the Study:

  • To present SwarmGenomics, a modular and user-friendly command-line pipeline.
  • To facilitate reference-based genome assembly and individual-based genetic analyses.
  • To lower the barrier for genomic analysis in diploid, non-model species.

Main Methods:

  • SwarmGenomics integrates seven modules: heterozygosity, runs of homozygosity, PSMC, unmapped reads, repeat analysis, mitochondrial genome assembly, and NUMT identification.
  • Modules can be run independently or as a complete workflow.
  • Demonstrated utility via a giant panda (Ailuropoda melanoleuca) case study.

Main Results:

  • The pipeline provides insights into genetic diversity, inbreeding history, and historical population size changes.
  • Analysis revealed transposable element activity and identified microbial contamination.
  • The giant panda case study showcased the pipeline's effectiveness.

Conclusions:

  • SwarmGenomics simplifies complex genomic analyses for non-model organisms.
  • It serves as a valuable research and teaching tool for population genetics and evolutionary biology.
  • The pipeline enhances accessibility to WGS data analysis.