ArticleBMC bioinformatics2017
De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
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Who cites it
12 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Applications of next-generation sequencing analysis for the detection of hepatocellular carcinoma-associated hepatitis B virus mutations.Journal of biomedical science · 2018Pooled it
- Genome-centric metagenomics reveals electroactive syntrophs in a conductive particle-dependent consortium from coastal sediments.Nature communications · 2026Article
- Reference-guided assembly of metagenomes with MetaCompass.Cell reports methods · 2025Article
- HBV DNA integration and somatic mutations in HCC patients with HBV-HCV dual infection reveals profiles intermediate between HBV- and HCV-related HCC.Journal of biomedical science · 2025Article
- Unraveling the role of hepatitis B virus DNA integration in B-cell lymphomagenesis.British journal of cancer · 2024Article
- Detection of HBV DNA integration in plasma cell-free DNA of different HBV diseases utilizing DNA capture strategy.Virologica Sinica · 2024Article
- HBV DNA Integration into Telomerase or MLL4 Genes and TERT Promoter Point Mutation as Three Independent Signatures in Subgrouping HBV-Related HCC with Distinct Features.Liver cancer · 2024Article
- Music of metagenomics-a review of its applications, analysis pipeline, and associated tools.Functional & integrative genomics · 2022Review
- ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data.BMC bioinformatics · 2021Article
- New approaches for metagenome assembly with short reads.Briefings in bioinformatics · 2020Review
- Microbial community analysis using high-throughput sequencing technology: a beginner's guide for microbiologists.Journal of microbiology (Seoul, Korea) · 2020Article
- Insights From Deep Sequencing of the HBV Genome-Unique, Tiny, and Misunderstood.Gastroenterology · 2019Review
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Authors and funding
8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThe accuracy of metagenomic assembly is usually compromised by high levels of polymorphism due to divergent reads from the same genomic region recognized as different loci when sequenced and assembled together. A viral quasispecies is a group of abundant and diversified genetically related viruses found in a single carrier. Current mainstream assembly methods, such as Velvet and SOAPdenovo, were not originally intended for the assembly of such metagenomics data, and therefore demands for new methods to provide accurate and informative assembly results for metagenomic data.
resultsIn this study, we present a hybrid method for assembling highly polymorphic data combining the partial de novo-reference assembly (PDR) strategy and the BLAST-based assembly pipeline (BBAP). The PDR strategy generates in situ reference sequences through de novo assembly of a randomly extracted partial data set which is subsequently used for the reference assembly for the full data set. BBAP employs a greedy algorithm to assemble polymorphic reads. We used 12 hepatitis B virus quasispecies NGS data sets from a previous study to assess and compare the performance of both PDR and BBAP. Analyses suggest the high polymorphism of a full metagenomic data set leads to fragmentized de novo assembly results, whereas the biased or limited representation of external reference sequences included fewer reads into the assembly with lower assembly accuracy and variation sensitivity. In comparison, the PDR generated in situ reference sequence incorporated more reads into the final PDR assembly of the full metagenomics data set along with greater accuracy and higher variation sensitivity. BBAP assembly results also suggest higher assembly efficiency and accuracy compared to other assembly methods. Additionally, BBAP assembly recovered HBV structural variants that were not observed amongst assembly results of other methods. Together, PDR/BBAP assembly results were significantly better than other compared methods.
conclusionsBoth PDR and BBAP independently increased the assembly efficiency and accuracy of highly polymorphic data, and assembly performances were further improved when used together. BBAP also provides nucleotide frequency information. Together, PDR and BBAP provide powerful tools for metagenomic data studies.
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