ArticleBMC bioinformatics2021
ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data.
Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 19 citations in OpenAlex.
- CRISPR spacers reveal diverse and abundant Thermococcales viruses in hydrothermal vents.Research square · 2026Article
- An evaluation of computational methods for reconstruction of human viral DNA genomes.GigaScience · 2026Article
- Virseqimprover: an integrated pipeline for viral contig error correction, extension, and annotation.PeerJ · 2025Article
- Sentinel Surveillance reveals phylogenetic diversity and detection of linear plasmids harboringAntimicrobial agents and chemotherapy · 2024Article
- COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes.Nature microbiology · 2024Article
- Exploring the Archaeal Virosphere by Metagenomics.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Highly divergent CRESS DNA and picorna-like viruses associated with bleached thalli of the green seaweedMicrobiology spectrum · 2023Article
- Article
- SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies.Microbiology spectrum · 2022Article
- Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
backgroundMetagenomics 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.
resultsTo 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.
conclusionsA 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.