Draft Genome Sequence of Streptococcus agalactiae KALRO-LC1 Strain Isolated from a Mastitis-Infected Camel in Laikipia County, Kenya

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ABSTRACT

We report the draft genome sequence of Streptococcus agalactiae KALRO-LC1 strain obtained from a mastitis-infected camel in Laikipia County, Kenya. The 2,201,604-bp draft genome is assembled into 3 contigs with a GC content of 35.87% and is predicted to contain 1,192 protein-coding sequences.

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QUAST: quality assessment tool for genome assemblies.

Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi … (2013)

Limitations of genome sequencing techniques have led to dozens of assembly algorithms, none of which is perfect. A number of methods for comparing assemblers have been developed, but none is yet a recognized benchmark. Further, most existing methods for comparing assemblies are only applicable to new assemblies of finished genomes; the problem of evaluating assemblies of previously unsequenced species has not been adequately considered. Here, we present QUAST-a quality assessment tool for evaluating and comparing genome assemblies. This tool improves on leading assembly comparison software with new ideas and quality metrics. QUAST can evaluate assemblies both with a reference genome, as well as without a reference. QUAST produces many reports, summary tables and plots to help scientists in their research and in their publications. In this study, we used QUAST to compare several genome assemblers on three datasets. QUAST tables and plots for all of them are available in the Supplementary Material, and interactive versions of these reports are on the QUAST website. http://bioinf.spbau.ru/quast . Supplementary data are available at Bioinformatics online.

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Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

Ryan Wick, Louise Judd, Claire Gorrie … (2017)

The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific Biosciences and Oxford Nanopore Technologies DNA sequencing platforms generate long reads that can produce complete genome assemblies, but the sequencing is more expensive and error-prone. There is significant interest in combining data from these complementary sequencing technologies to generate more accurate “hybrid” assemblies. However, few tools exist that truly leverage the benefits of both types of data, namely the accuracy of short reads and the structural resolving power of long reads. Here we present Unicycler, a new tool for assembling bacterial genomes from a combination of short and long reads, which produces assemblies that are accurate, complete and cost-effective. Unicycler builds an initial assembly graph from short reads using the de novo assembler SPAdes and then simplifies the graph using information from short and long reads. Unicycler uses a novel semi-global aligner to align long reads to the assembly graph. Tests on both synthetic and real reads show Unicycler can assemble larger contigs with fewer misassemblies than other hybrid assemblers, even when long-read depth and accuracy are low. Unicycler is open source (GPLv3) and available at github.com/rrwick/Unicycler.

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NCBI prokaryotic genome annotation pipeline

Tatiana Tatusova, Michael DiCuccio, Azat Badretdin … (2016)

Recent technological advances have opened unprecedented opportunities for large-scale sequencing and analysis of populations of pathogenic species in disease outbreaks, as well as for large-scale diversity studies aimed at expanding our knowledge across the whole domain of prokaryotes. To meet the challenge of timely interpretation of structure, function and meaning of this vast genetic information, a comprehensive approach to automatic genome annotation is critically needed. In collaboration with Georgia Tech, NCBI has developed a new approach to genome annotation that combines alignment based methods with methods of predicting protein-coding and RNA genes and other functional elements directly from sequence. A new gene finding tool, GeneMarkS+, uses the combined evidence of protein and RNA placement by homology as an initial map of annotation to generate and modify ab initio gene predictions across the whole genome. Thus, the new NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) relies more on sequence similarity when confident comparative data are available, while it relies more on statistical predictions in the absence of external evidence. The pipeline provides a framework for generation and analysis of annotation on the full breadth of prokaryotic taxonomy. For additional information on PGAP see https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ and the NCBI Handbook, https://www.ncbi.nlm.nih.gov/books/NBK174280/.

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Author and article information

Contributors

Edwin Murungi:

ORCID: https://orcid.org/0000-0001-9896-0664

Steven R. Gill: Role: Editor

Journal

Journal ID (nlm-ta): Microbiol Resour Announc

Journal ID (iso-abbrev): Microbiol Resour Announc

Journal ID (publisher-id): mra

Title: Microbiology Resource Announcements

Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )

ISSN (Electronic): 2576-098X

Publication date (Electronic, pub): 19 September 2022

Publication date (Electronic, collection): October 2022

Publication date PMC-release: 19 September 2022

Volume: 11

Issue: 10

Electronic Location Identifier: e00910-22

Affiliations

[a ] Department of Medical Biochemistry, Kisii University, Kisii, Kenya

[b ] Veterinary Research Institute, Kenya Agricultural and Livestock Research Organization, Muguga, Kenya

[c ] School of Health Sciences, Meru University of Science and Technology, Meru, Kenya

University of Rochester School of Medicine and Dentistry

Author notes

The authors declare no conflict of interest.

Author information

Edwin Murungi https://orcid.org/0000-0001-9896-0664

Article

Publisher ID: 00910-22 Publisher ID: mra.00910-22

DOI: 10.1128/mra.00910-22

PMC ID: 9584315

PubMed ID: 36121236

SO-VID: dd65c057-c5d1-470c-99e0-3d9b6bf302bf

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

History

Date received : 1 September 2022

Date accepted : 3 September 2022

Page count

Figures: 0, Tables: 1, Equations: 0, References: 16, Pages: 2, Words: 1232

Funding

Funded by: EU-AgriFI;

Award ID: Climate Smart Agricultural Productivity Project

Award Recipient : Monicah Maichomo

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cover-date October 2022

Data availability:

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Draft Genome Sequence of Streptococcus agalactiae KALRO-LC1 Strain Isolated from a Mastitis-Infected Camel in Laikipia County, Kenya

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ABSTRACT

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Genome Integrity

Most cited references 15

QUAST: quality assessment tool for genome assemblies.

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

NCBI prokaryotic genome annotation pipeline

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