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Updated: Mar 3, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline.

Sonia Agrawal¹, Cesar Arze¹, Ricky S Adkins¹

¹Institute for Genome Sciences, Baltimore, MD, USA.

|April 29, 2017

Summary

This summary is machine-generated.

CloVR-Comparative offers an automated, cloud-based pipeline for microbial genomics, simplifying comparative analysis. This tool makes complex genomic sequence analysis accessible to researchers without extensive bioinformatics expertise.

Keywords:

Automated analysis Bioinformatics resource Cloud computing Comparative genomics Microbial genomics Virtual machine Whole-genome alignment

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Published on: April 4, 2018

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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Area of Science:

Microbial Genomics
Bioinformatics
Computational Biology

Background:

Genomic sequence data is rapidly increasing, necessitating accessible bioinformatics support.
Scalable and user-friendly tools are crucial for the scientific community to leverage genomic data.
CloVR-Comparative addresses this need by integrating common bioinformatics tools into an automated pipeline.

Purpose of the Study:

To develop an intuitive, automated, and cloud-enabled bioinformatics pipeline for comparative microbial genomics.
To simplify the analysis of genomic sequence data for a wider scientific audience.

Main Methods:

CloVR-Comparative processes user-uploaded or NCBI-downloaded annotated complete or draft genome sequences.
It performs reference-free multiple whole-genome alignments to identify unique, shared, and core coding sequences (CDSs) and single nucleotide polymorphisms (SNPs).
The pipeline is managed via a web interface and distributed as a virtual appliance compatible with local computers and cloud platforms (Amazon EC2).

Main Results:

The pipeline generates summary reports, detailed results files, and graphical visualizations, including phylogenetic trees and circular figures.
A database file linked to the Sybil comparative genome browser is provided for enhanced data exploration.
Analysis of 40 Escherichia coli genomes completed in under 36 hours on a local desktop or at a cost of less than $20 on EC2.

Conclusions:

CloVR-Comparative democratizes comparative genomics by enabling users with internet access to conduct projects.
It eliminates the requirement for on-site computational resources and specialized bioinformatics expertise.