ArticleScientific reports2015
Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the "Finished" C. elegans Genome.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Molecular life sciences in the era of the Fourth Industrial Revolution: sequencing, multi-omics and artificial intelligence.Emerging topics in life sciences · 2025Review
- CGC1, a new reference genome forGenome research · 2025Article
- The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases.Genome research · 2025Review
- Isolation, molecular identification, and genomic analysis ofFrontiers in microbiology · 2024Article
- The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods.Foods (Basel, Switzerland) · 2022Review
- Genomic architecture of 5S rDNA cluster and its variations within and between species.BMC genomics · 2022Article
- G-quadruplexes in helminth parasites.Nucleic acids research · 2022Article
- Formation of artificial chromosomes in Caenorhabditis elegans and analyses of their segregation in mitosis, DNA sequence composition and holocentromere organization.Nucleic acids research · 2021Article
- Comprehensive Wet-Bench and Bioinformatics Workflow for Complex Microbiota Using Oxford Nanopore Technologies.mSystems · 2021Article
- A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome.Experimental & molecular medicine · 2021Article
- Steroid hormones sulfatase inactivation extends lifespan and ameliorates age-related diseases.Nature communications · 2021Article
- Article
- Long-read human genome sequencing and its applications.Nature reviews. Genetics · 2020Review
- Opportunities and challenges in long-read sequencing data analysis.Genome biology · 2020Review
- Direct full-length RNA sequencing reveals unexpected transcriptome complexity duringGenome research · 2020Article
- Article
- A new reference genome sequence for Caenorhabditis elegans?Lab animal · 2019Article
- Recompleting theGenome research · 2019Article
- Technological advances in maize breeding: past, present and future.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Review
- Linked read technology for assembling large complex and polyploid genomes.BMC genomics · 2018Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Most next-generation sequencing platforms permit acquisition of high-throughput DNA sequences, but the relatively short read length limits their use in genome assembly or finishing. Illumina has recently released a technology called Synthetic Long-Read Sequencing that can produce reads of unusual length, i.e., predominately around 10 Kb. However, a systematic assessment of their use in genome finishing and assembly is still lacking. We evaluate the promise and deficiency of the long reads in these aspects using isogenic C. elegans genome with no gap. First, the reads are highly accurate and capable of recovering most types of repetitive sequences. However, the presence of tandem repetitive sequences prevents pre-assembly of long reads in the relevant genomic region. Second, the reads are able to reliably detect missing but not extra sequences in the C. elegans genome. Third, the reads of smaller size are more capable of recovering repetitive sequences than those of bigger size. Fourth, at least 40 Kbp missing genomic sequences are recovered in the C. elegans genome using the long reads. Finally, an N50 contig size of at least 86 Kbp can be achieved with 24 × reads but with substantial mis-assembly errors, highlighting a need for novel assembly algorithm for the long reads.
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