ArticleFrontiers in genetics2020
PacBio Long Reads Improve Metagenomic Assemblies, Gene Catalogs, and Genome Binning.
Article in Frontiers in genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Changes in Alternative Splicing are Associated with Insecticide Response and Resistance.Genome biology and evolution · 2026Article
- Gut check: Exploring tools, techniques, and future directions in microbiome research.Poultry science · 2026Article
- Chromosome-level genome assembly of Neoseiulus longispinosus (Phytoseiidae).Scientific data · 2026Article
- Opportunities for RNA sequencing in physiology: from big data to understanding homeostasis and heterogeneity.Function (Oxford, England) · 2026Review
- HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.Nucleic acids research · 2026Article
- Metagenomic next-generation sequencing: new horizons in microbiology.Frontiers in cellular and infection microbiology · 2026Review
- Metagenomic Applications to Herbivore Gut Microbiomes: A Comprehensive Review of Microbial Diversity and Host Interactions.Animals : an open access journal from MDPI · 2025Review
- Metagenomic assemblies tend to break around antibiotic resistance genes.BMC genomics · 2024Article
- The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies.Microbial genomics · 2024Article
- Unraveling metagenomics through long-read sequencing: a comprehensive review.Journal of translational medicine · 2024Review
- Sample and Library Preparation for PacBio Long-Read Sequencing in Grapevine.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A metagenomic approach to demystify the anaerobic digestion black box and achieve higher biogas yield: a review.Frontiers in microbiology · 2024Review
- Present and future outlooks on environmental DNA-based methods for antibiotic discovery.Current opinion in microbiology · 2023Review
- Biosynthetic gene cluster synteny: Orthologous polyketide synthases in Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata.MicrobiologyOpen · 2023Article
- Comparing genomes recovered from time-series metagenomes using long- and short-read sequencing technologies.Microbiome · 2023Article
- Biosynthetic Potential ofJournal of fungi (Basel, Switzerland) · 2023Article
- DL-TODA: A Deep Learning Tool for Omics Data Analysis.Biomolecules · 2023Article
- Pitfalls of genotyping microbial communities with rapidly growing genome collections.Cell systems · 2023Article
- Application of emerging technologies for gut microbiome research.Singapore medical journal · 2023Review
- Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
PacBio long reads sequencing presents several potential advantages for DNA assembly, including being able to provide more complete gene profiling of metagenomic samples. However, lower single-pass accuracy can make gene discovery and assembly for low-abundance organisms difficult. To evaluate the application and performance of PacBio long reads and Illumina HiSeq short reads in metagenomic analyses, we directly compared various assemblies involving PacBio and Illumina sequencing reads based on two anaerobic digestion microbiome samples from a biogas fermenter. Using a PacBio platform, 1.58 million long reads (19.6 Gb) were produced with an average length of 7,604 bp. Using an Illumina HiSeq platform, 151.2 million read pairs (45.4 Gb) were produced. Hybrid assemblies using PacBio long reads and HiSeq contigs produced improvements in assembly statistics, including an increase in the average contig length, contig N50 size, and number of large contigs. Interestingly, depth-based hybrid assemblies generated a higher percentage of complete genes (98.86%) compared to those based on HiSeq contigs only (40.29%), because the PacBio reads were long enough to cover many repeating short elements and capture multiple genes in a single read. Additionally, the incorporation of PacBio long reads led to considerable advantages regarding reducing contig numbers and increasing the completeness of the genome reconstruction, which was poorly assembled and binned when using HiSeq data alone. From this comparison of PacBio long reads with Illumina HiSeq short reads related to complex microbiome samples, we conclude that PacBio long reads can produce longer contigs, more complete genes, and better genome binning, thereby offering more information about metagenomic samples.
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Registered trials
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