LTR Assembly Index (LAI) is a reference-free genome metric that evaluates assembly continuity using LTR-RTs. LTR retrotransposons (LTR-RTs) are the predominant interspersed repeat that is poorly assembled in draft genomes. Correcting for LTR-RT amplification dynamics, LAI is independent of genome size, genomic LTR-RT content, and gene space evaluation metrics such as BUSCO. LAI = Raw LAI + 2.8138 × (94 – whole genome LTR identity). The LAI is set to 0 when raw LAI = 0 or the adjustment produces a negative value. Raw LAI = (Intact LTR element length / Total LTR sequence length) * 100

Reference:

Shujun Ou, Jinfeng Chen, Ning Jiang, Assessing genome assembly quality using the LTR Assembly Index (LAI), Nucleic Acids Research, Volume 46, Issue 21, 30 November 2018, Page e126, 10.1093/nar/gky730

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