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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.

Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Maxam-Gilbert Sequencing

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
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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.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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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...

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Related Experiment Video

Updated: May 23, 2026

Metagenomic Analysis of Silage

Metagenomic Analysis of Silage

Published on: January 13, 2017

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

Anton Bankevich¹, Sergey Nurk, Dmitry Antipov

¹Algorithmic Biology Laboratory, St. Petersburg Academic University, Russian Academy of Sciences, St. Petersburg, Russia.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology

|April 18, 2012

Summary

SPAdes is a new software tool that assembles genomes from single bacterial cells. This advances genomics by enabling the study of uncultivated bacteria, overcoming limitations of current sequencing technologies.

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Last Updated: May 23, 2026

Metagenomic Analysis of Silage

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Published on: January 13, 2017

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

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Area of Science:

Microbiology
Genomics
Bioinformatics

Background:

Most bacteria are uncultivable, limiting genomic study.
Metagenomics provides gene-level data but lacks whole-genome assemblies.
Single-cell genomics aims to fill this gap by assembling genomes from individual cells.

Purpose of the Study:

To develop a novel assembler for single-cell and standard (multicell) genomic data.
To improve the quality and completeness of whole-genome assemblies from uncultivated bacteria.

Main Methods:

Development of the SPAdes assembler, a new algorithm for genome assembly.
Comparative analysis of SPAdes against existing single-cell (E+V-SC) and multicell (Velvet, SoapDeNovo) assemblers.
Evaluation of assembly performance using metrics relevant to single-cell data challenges (coverage, errors, chimeras).

Main Results:

SPAdes demonstrates superior performance in generating single-cell assemblies compared to E+V-SC.
SPAdes also shows improved results for standard multicell assembly over Velvet and SoapDeNovo.
The software enables the recovery of genomic information from previously uncultivable bacteria.

Conclusions:

SPAdes significantly advances the field of single-cell genomics.
It provides a powerful tool for obtaining whole-genome assemblies of uncultivated organisms.
This opens new avenues for understanding microbial diversity and function.