ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data
Autor: | Zachary Deng, Eric Delwart |
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Jazyk: | angličtina |
Rok vydání: | 2021 |
Předmět: |
Viral metagenomics
Microbial Genomes Base pair Computer science Sequence assembly Pathogen detection Computational biology Genome Viral lcsh:Computer applications to medicine. Medical informatics Biochemistry Genome 03 medical and health sciences Structural Biology De novo assembly Animals Humans Next-Gen Sequencing Molecular Biology lcsh:QH301-705.5 030304 developmental biology 0303 health sciences Contig Applied Mathematics 030302 biochemistry & molecular biology Viral discovery Chromosome High-Throughput Nucleotide Sequencing food and beverages Sequence Analysis DNA Computer Science Applications lcsh:Biology (General) Metagenomics Metagenome lcsh:R858-859.7 DNA microarray Software Algorithms |
Zdroj: | BMC Bioinformatics, Vol 22, Iss 1, Pp 1-19 (2021) BMC Bioinformatics |
ISSN: | 1471-2105 |
Popis: | Background Metagenomics is the study of microbial genomes for pathogen detection and discovery in human clinical, animal, and environmental samples via Next-Generation Sequencing (NGS). Metagenome de novo sequence assembly is a crucial analytical step in which longer contigs, ideally whole chromosomes/genomes, are formed from shorter NGS reads. However, the contigs generated from the de novo assembly are often very fragmented and rarely longer than a few kilo base pairs (kb). Therefore, a time-consuming extension process is routinely performed on the de novo assembled contigs. Results To facilitate this process, we propose a new tool for metagenome contig extension after de novo assembly. ContigExtender employs a novel recursive extending strategy that explores multiple extending paths to achieve highly accurate longer contigs. We demonstrate that ContigExtender outperforms existing tools in synthetic, animal, and human metagenomics datasets. Conclusions A novel software tool ContigExtender has been developed to assist and enhance the performance of metagenome de novo assembly. ContigExtender effectively extends contigs from a variety of sources and can be incorporated in most viral metagenomics analysis pipelines for a wide variety of applications, including pathogen detection and viral discovery. |
Databáze: | OpenAIRE |
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