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Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

RNA-seq

RNA-seq

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...

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Alvis: a tool for contig and read ALignment VISualisation and chimera detection.

Samuel Martin¹, Richard M Leggett²

¹Earlham Institute, Norwich Research Park, Norwich, UK.

BMC Bioinformatics

|March 17, 2021

Summary

Alvis is a command-line tool that creates visualizations for alignment data. It aids in understanding assembly quality, identifying errors like chimeric reads, and improving genome assembly contiguity.

Keywords:

Chimera detection Genomics Sequence alignment Visualisation

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Alignment analysis against reference genomes is crucial for long reads, assembly assessment, and target capture data.
Automated parsing of aligner outputs is common, but human inspection of individual alignments offers deeper insights.
Visualizations are valuable for communicating complex assembly results effectively.

Purpose of the Study:

To develop a user-friendly command-line tool for generating visualizations of alignment analysis.
To enhance the understanding and assessment of genome assembly quality through visual aids.
To identify and address common sources of misassemblies, such as chimeric reads.

Main Methods:

Developed Alvis, a fast and portable command-line tool.
Alvis accepts multiple alignment input formats.
Generates production-ready vector images for visualization and analysis.

Main Results:

Alvis provides visualizations for common alignment analysis tasks.
The tool highlights potentially chimeric reads or contigs, which are frequent causes of misassemblies.
Output is in production-ready vector image format.

Conclusions:

Alvis diagrams improve understanding of assembly quality and enable visualization of read coverage.
The tool facilitates the identification of potential errors in genome assemblies.
Splitting chimeric reads using Alvis output can enhance assembly contiguity while preserving correctness.