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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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Updated: May 15, 2025

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

CoverM: read alignment statistics for metagenomics.

Samuel T N Aroney¹, Rhys J P Newell¹, Jakob N Nissen²

¹Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba 4102, Australia.

Bioinformatics (Oxford, England)

|April 7, 2025

Summary

This summary is machine-generated.

CoverM is a new software package that unifies and simplifies the calculation of microbial genome coverage statistics from metagenomic data. This tool enhances the analysis of microbial communities by providing flexible and efficient coverage estimations.

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Area of Science:

Microbiology
Bioinformatics
Genomics

Background:

Genome-centric analysis of metagenomic samples is crucial for understanding microbial community function.
Calculating read coverage is essential for genome recovery and community composition estimation.
Existing methods for coverage calculation are often ad-hoc and vary between software packages.

Purpose of the Study:

To present CoverM, a unified software package for calculating coverage statistics.
To provide an ergonomic and flexible solution for metagenomic data analysis.
To improve the efficiency and consistency of coverage calculations.

Main Methods:

CoverM calculates various coverage statistics for contigs and genomes.
It utilizes "Mosdepth arrays" for computational efficiency.
Coverage statistics are derived from streamed read alignment results, minimizing I/O overhead.

Main Results:

CoverM offers a unified approach to calculating per-reference coverage.
The software provides ergonomic and flexible coverage statistics.
It enhances computational efficiency and reduces I/O operations.

Conclusions:

CoverM offers a powerful and unified solution for calculating genome coverage in metagenomic studies.
The software improves efficiency and flexibility in analyzing microbial community composition and function.
It standardizes coverage calculation, facilitating more reliable downstream analyses.