DBBQs: dataBase of Bacterial Quality scores

Visanu Wanchai,Intawat Nookaew,David Ussery,Preecha Patumcharoenpol

doi:10.1186/s12859-017-1900-9

Visanu Wanchai, Intawat Nookaew + Show 2 more

Open Access

https://doi.org/10.1186/s12859-017-1900-9

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Journal: BMC bioinformatics	Publication Date: Dec 1, 2017
Citations: 8	License type: open-access

Affiliation: University of Arkansas for Medical Sciences

Abstract

BackgroundIt is well-known that genome sequencing technologies are becoming significantly cheaper and faster. As a result of this, the exponential growth in sequencing data in public databases allows us to explore ever growing large collections of genome sequences. However, it is less known that the majority of available sequenced genome sequences in public databases are not complete, drafts of varying qualities. We have calculated quality scores for around 100,000 bacterial genomes from all major genome repositories and put them in a fast and easy-to-use database.ResultsProkaryotic genomic data from all sources were collected and combined to make a non-redundant set of bacterial genomes. The genome quality score for each was calculated by four different measurements: assembly quality, number of rRNA and tRNA genes, and the occurrence of conserved functional domains. The dataBase of Bacterial Quality scores (dBBQs) was designed to store and retrieve quality scores. It offers fast searching and download features which the result can be used for further analysis. In addition, the search results are shown in interactive JavaScript chart framework using DC.js. The analysis of quality scores across major public genome databases find that around 68% of the genomes are of acceptable quality for many uses.ConclusionsdBBQs (available at http://arc-gem.uams.edu/dbbqs) provides genome quality scores for all available prokaryotic genome sequences with a user-friendly Web-interface. These scores can be used as cut-offs to get a high-quality set of genomes for testing bioinformatics tools or improving the analysis. Moreover, all data of the four measurements that were combined to make the quality score for each genome, which can potentially be used for further analysis. dBBQs will be updated regularly and is freely use for non-commercial purpose.

Highlights

It is well-known that genome sequencing technologies are becoming significantly cheaper and faster
The exponential growth in sequencing data in public databases allow us to explore through large collections of genome sequences [2]
It is less known that many genomes in public databases are left as draft genome sequences

Summary

Introduction

It is well-known that genome sequencing technologies are becoming significantly cheaper and faster. As a result of this, the exponential growth in sequencing data in public databases allows us to explore ever growing large collections of genome sequences. It is less known that the majority of available sequenced genome sequences in public databases are not complete, drafts of varying qualities. It is well known that the current state-of-art of sequencing technologies makes genome sequencing significantly cheaper and quicker. The exponential growth in sequencing data in public databases allow us to explore through large collections of genome sequences [2]. It is less known that many genomes in public databases are left as draft genome sequences. A huge number of draft genomes usually comes from difficulty of finishing process of genome sequences generated by second generation sequencing machine. Many genome projects on major genome repositories were left unfinished [3]

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