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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...

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.
Challenges of the Maxam-Gilbert Method
The...

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Related Experiment Video

Updated: Dec 6, 2025

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

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

Published on: August 20, 2021

metaFlye: scalable long-read metagenome assembly using repeat graphs.

Mikhail Kolmogorov¹, Derek M Bickhart², Bahar Behsaz³

¹Department of Computer Science and Engineering, University of California, San Diego, CA, USA.

|October 6, 2020

Summary

This summary is machine-generated.

MetaFlye significantly improves long-read metagenomic assembly, producing more complete and contiguous bacterial genomes from complex samples like microbiomes. This advancement aids in discovering novel natural products.

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G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

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Published on: March 22, 2018

Large-Scale Screens of Metagenomic Libraries

Large-Scale Screens of Metagenomic Libraries

Published on: May 28, 2007

Related Experiment Videos

Last Updated: Dec 6, 2025

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

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

Published on: August 20, 2021

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

Large-Scale Screens of Metagenomic Libraries

Large-Scale Screens of Metagenomic Libraries

Published on: May 28, 2007

Area of Science:

Genomics and Bioinformatics
Microbiome Research
Metagenomics

Background:

Long-read sequencing enhances bacterial genome assembly compared to short-read methods.
Assembling complex metagenomic data remains a challenge for current long-read assemblers.
Challenges include uneven community composition and intra-species genetic variation.

Purpose of the Study:

To introduce metaFlye, a novel long-read metagenomic assembler.
To address challenges in assembling complex metagenomic datasets.
To improve the completeness and contiguity of bacterial genome assemblies from microbiomes.

Main Methods:

Benchmarking metaFlye on simulated and mock bacterial communities.
Applying metaFlye to long-read sequenced sheep and human microbiomes.
Evaluating assembly performance against state-of-the-art long-read assemblers.

Main Results:

MetaFlye consistently achieved superior completeness and contiguity in assemblies.
Reconstructed 63 complete or near-complete bacterial genomes from the sheep microbiome.
Enabled discovery of full-length biosynthetic gene clusters in human microbiomes.

Conclusions:

MetaFlye offers a robust solution for long-read metagenomic assembly challenges.
Facilitates high-quality genome reconstruction from complex microbial communities.
Supports the discovery of novel bioactive natural products through comprehensive microbiome analysis.