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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.

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Updated: Jun 28, 2026

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion

Published on: June 25, 2017

SCAPP: an algorithm for improved plasmid assembly in metagenomes.

David Pellow¹, Alvah Zorea², Maraike Probst³

¹Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, 6997801, Israel. dpellow@post.tau.ac.il.

|June 26, 2021

Summary

This summary is machine-generated.

SCAPP is a new tool that assembles plasmid DNA sequences from metagenomic data. This computational advance improves the analysis of plasmids, which often carry antibiotic resistance genes.

Keywords:

Assembly Plasmids

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Area of Science:

Microbiology
Bioinformatics
Genomics

Background:

Metagenomic sequencing identifies many bacterial genomes, often containing plasmids.
Plasmids are small DNA molecules that can transfer between bacteria and confer antibiotic resistance.
Current computational tools for analyzing plasmids in metagenomic samples are insufficient.

Purpose of the Study:

To develop an improved algorithm and tool for assembling plasmid sequences from metagenomic data.
To address the limitations of existing tools in plasmid analysis.

Main Methods:

Developed SCAPP (Sequence Contents-Aware Plasmid Peeler), a Python package for plasmid assembly.
Integrated biological knowledge about plasmids into the SCAPP algorithm.
Compared SCAPP's performance against Recycler and metaplasmidSPAdes using simulated and real-world datasets, including a novel assessment procedure with parallel sequencing data.

Main Results:

SCAPP demonstrated superior performance compared to Recycler and metaplasmidSPAdes across various datasets.
The tool successfully assembled full plasmid sequences from metagenomic samples.
SCAPP identified novel and clinically relevant plasmids in generated datasets, including a human gut plasmidome.

Conclusions:

SCAPP is a user-friendly Python package for assembling plasmid sequences from metagenomic samples.
The tool offers improved performance over existing metagenomic plasmid assemblers.
SCAPP facilitates the discovery of novel and clinically significant plasmids, enhancing our understanding of microbial communities.