Assessing genome assembly quality using the LTR Assembly Index (LAI)
By Shujun Ou, Jinfeng Chen, Ning Jiang. Nucleic Acids Research, 2018
765 citations recorded by the source corpus.
Abstract Assembling a plant genome is challenging due to the abundance of repetitive sequences, yet no standard is available to evaluate the assembly of repeat space. LTR retrotransposons (LTR-RTs) are the predominant interspersed repeat that is poorly assembled in draft genomes. Here, we propose a reference-free genome metric called LTR Assembly Index (LAI) that evaluates assembly continuity using LTR-RTs. After correcting for LTR-RT amplification dynamics, we show that LAI is independent of genome size, genomic LTR-RT content, and gene space evaluation metrics (i.e., BUSCO and CEGMA). By comparing genomic sequences produced by various sequencing techniques, we reveal the significant gain of assembly continuity by using long-read-based techniques over short-read-based methods. Moreover, LAI can facilitate iterative assembly improvement with assembler selection and identify low-quality genomic regions. To apply LAI, intact LTR-RTs and total LTR-RTs should contribute at least 0.1% and 5% to the genome size, respectively. The LAI program is freely available on GitHub: https://github.com/oushujun/LTR_retriever.
Subfields: Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/3da28fdd520d26ce72b3b879d8376d71ff8706ef
How researchers see this paper
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In Molecular Biology
- Jeb Rosen
- Arian F. A. Smit
- Robert M. Hubley
- Andrew G. Clark
- Jullien M. Flynn
- Clément Goubert
- Cédric Feschotte
- Shujun Ou
In Plant Science
- Shujun Ou
- Ning Jiang
- Jeb Rosen
- Arian F. A. Smit
- Robert M. Hubley
- Cédric Feschotte
- Andrew G. Clark
- Jullien M. Flynn
Citations in the corpus
- Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline (2019, background): “[8] demonstrated that the assembly contiguity of repetitive sequences in recent 53 long-read assemblies is even better than traditional BAC-based reference genomes.”
- RepeatModeler2 for automated genomic discovery of transposable element families (2020, methodology): “Notably, we integrated an optional module dedicated to the identification of LTR elements in the genome through their structural characteristics (30, 31).”