ArticleGigaScience2019
Assessment of human diploid genome assembly with 10x Linked-Reads data.
Article in GigaScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Enhancing variant detection in complex genomes: leveraging linked reads for robust SNP, Indel, and structural variant analysis.Research square · 2026Article
- A little longer, a lot better: simulation-guided exploration of extended-length single-end barcoded reads for structural variant detection.Bioinformatics advances · 2026Article
- Genome assemblies of IndianNAR genomics and bioinformatics · 2025Article
- Genomic resources for comparative analyses of obligate avian brood parasitism.bioRxiv : the preprint server for biology · 2025Article
- The Bioinformatic Applications of Hi-C and Linked Reads.Genomics, proteomics & bioinformatics · 2024Review
- Somatic mutation phasing and haplotype extension using linked-reads in multiple myeloma.bioRxiv : the preprint server for biology · 2024Article
- An efficient molecular genetic testing strategy for incontinentia pigmenti based on single-tube long fragment read sequencing.NPJ genomic medicine · 2024Article
- LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome.GigaScience · 2024Article
- Genomic evidence of sex chromosome aneuploidy and infection-associated genotypes in the tsetse fly Glossina fuscipes, the major vector of African trypanosomiasis in Uganda.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2023Article
- Deciphering complex breakage-fusion-bridge genome rearrangements with Ambigram.Nature communications · 2023Article
- SpecHap: a diploid phasing algorithm based on spectral graph theory.Nucleic acids research · 2021Article
- Aquila enables reference-assisted diploid personal genome assembly and comprehensive variant detection based on linked reads.Nature communications · 2021Article
- Article
- URMAP, an ultra-fast read mapper.PeerJ · 2020Article
- Assessment of human diploid genome assembly with 10x Linked-Reads data.GigaScience · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundProducing cost-effective haplotype-resolved personal genomes remains challenging. 10x Linked-Read sequencing, with its high base quality and long-range information, has been demonstrated to facilitate de novo assembly of human genomes and variant detection. In this study, we investigate in depth how the parameter space of 10x library preparation and sequencing affects assembly quality, on the basis of both simulated and real libraries.
resultsWe prepared and sequenced eight 10x libraries with a diverse set of parameters from standard cell lines NA12878 and NA24385 and performed whole-genome assembly on the data. We also developed the simulator LRTK-SIM to follow the workflow of 10x data generation and produce realistic simulated Linked-Read data sets. We found that assembly quality could be improved by increasing the total sequencing coverage (C) and keeping physical coverage of DNA fragments (CF) or read coverage per fragment (CR) within broad ranges. The optimal physical coverage was between 332× and 823× and assembly quality worsened if it increased to >1,000× for a given C. Long DNA fragments could significantly extend phase blocks but decreased contig contiguity. The optimal length-weighted fragment length (W${\mu _{FL}}$) was ∼50-150 kb. When broadly optimal parameters were used for library preparation and sequencing, ∼80% of the genome was assembled in a diploid state.
conclusionsThe Linked-Read libraries we generated and the parameter space we identified provide theoretical considerations and practical guidelines for personal genome assemblies based on 10x Linked-Read sequencing.
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