ArticleNature communications2021
Aquila enables reference-assisted diploid personal genome assembly and comprehensive variant detection based on linked reads.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- gSV: a general structural variant detector using the third-generation sequencing data.Briefings in bioinformatics · 2026Article
- 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
- The Bioinformatic Applications of Hi-C and Linked Reads.Genomics, proteomics & bioinformatics · 2024Review
- LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome.GigaScience · 2024Article
- BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies.Nucleic acids research · 2023Article
- Aquila enables reference-assisted diploid personal genome assembly and comprehensive variant detection based on linked reads.Nature communications · 2021Article
- Aquila_stLFR: diploid genome assembly based structural variant calling package for stLFR linked-reads.Bioinformatics advances · 2021Article
- stLFRsv: A Germline Structural Variant Analysis Pipeline Using Co-barcoded Reads.Frontiers in genetics · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We introduce Aquila, a new approach to variant discovery in personal genomes, which is critical for uncovering the genetic contributions to health and disease. Aquila uses a reference sequence and linked-read data to generate a high quality diploid genome assembly, from which it then comprehensively detects and phases personal genetic variation. The contigs of the assemblies from our libraries cover >95% of the human reference genome, with over 98% of that in a diploid state. Thus, the assemblies support detection and accurate genotyping of the most prevalent types of human genetic variation, including single nucleotide polymorphisms (SNPs), small insertions and deletions (small indels), and structural variants (SVs), in all but the most difficult regions. All heterozygous variants are phased in blocks that can approach arm-level length. The final output of Aquila is a diploid and phased personal genome sequence, and a phased Variant Call Format (VCF) file that also contains homozygous and a few unphased heterozygous variants. Aquila represents a cost-effective approach that can be applied to cohorts for variation discovery or association studies, or to single individuals with rare phenotypes that could be caused by SVs or compound heterozygosity.
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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 Socratic graph.