Calculated LAI is too large

Question

[Yao]

I have post the issue in LTR_retriever Github issue (https://github.com/oushujun/LTR_retriever/issues/171), but I would like to collect more opinion.

Thank you for your effort on these tools, I am using EDTA (v2.2.1) to carry out de novo TE annotation. After I used EDTA output file fasta.mod.EDTA.raw/LTR/.fasta.mod.pass.list and .fasta.mod.EDTA.anno/.fasta.mod.out as input to calculate LAI, but the LAI seemed abnormal:

Chr From    To  Intact  Total   raw_LAI LAI
whole_genome    1   521293298   0.0515  0.0667  77.13   74.94
Chr01_hap1  1   3000000 0.0355  0.0234  100.1   97.91
Chr01_hap1  300001  3300000 0.0423  0.0256  100.1   97.91
Chr01_hap1  600001  3600000 0.0475  0.0277  100.1   97.91
Chr01_hap1  900001  3900000 0.0475  0.0285  100.1   97.91
Chr01_hap1  1200001 4200000 0.0415  0.0262  100.1   97.91

For another haplotype:

Chr From    To  Intact  Total   raw_LAI LAI
whole_genome    1   503369137   0.0497  0.0594  83.75   82.73
Chr01_hap2  1   3000000 0.0285  0.0232  100.1   99.08
Chr01_hap2  300001  3300000 0.0263  0.0277  94.79   93.77
Chr01_hap2  600001  3600000 0.0311  0.0299  100.1   99.08
Chr01_hap2  900001  3900000 0.0287  0.0286  100.1   99.08
Chr01_hap2  1200001 4200000 0.0287  0.0277  100.1   99.08
Chr01_hap2  1500001 4500000 0.0303  0.0293  100.1   99.08
Chr01_hap2  1800001 4800000 0.0289  0.0283  100.1   99.08
Chr01_hap2  2100001 5100000 0.0297  0.0289  100.1   99.08
Chr01_hap2  2400001 5400000 0.0197  0.0284  69.32   68.30
Chr01_hap2  2700001 5700000 0.0214  0.0315  67.83   66.81
Chr01_hap2  3000001 6000000 0.0212  0.0304  69.72   68.70

Here is the log of LAI:

######################################
### LTR Assembly Index (LAI) beta3.2 ###
######################################

Developer: Shujun Ou

Please cite:

Ou S., Chen J. and Jiang N. (2018). Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Res. gky730: https://doi.org/10.1093/nar/gky730

Parameters: -t 64 -genome /dssg/home/acct-jiang.lu/jiang.lu/.yaoxk_dir/genome_denovo/SH/04-asm/03-final/hap2/Vitis_amurensis_ShuangHong_hap2.fasta -intact /dssg/home/acct-jiang.lu/jiang.lu/.yaoxk_dir/genome_denovo/SH/05-ant/01-repeat/hap2/repeat_library/TE/Vitis_amurensis_ShuangHong_hap2.fasta.mod.EDTA.raw/LTR/Vitis_amurensis_ShuangHong_hap2.fasta.mod.pass.list -all /dssg/home/acct-jiang.lu/jiang.lu/.yaoxk_dir/genome_denovo/SH/05-ant/01-repeat/hap2/repeat_library/TE/Vitis_amurensis_ShuangHong_hap2.fasta.mod.EDTA.anno/Vitis_amurensis_ShuangHong_hap2.fasta.mod.out


Tue May 21 13:29:55 CST 2024    Dependency checking: Passed!
Tue May 21 13:29:55 CST 2024    Calculation of LAI will be based on the whole genome.
                Please use the -mono parameter if your genome is a recent ployploid, otherwise high identity between LTR homeologues will overcorrect raw LAI scores and result in low LAI.
Tue May 21 13:29:55 CST 2024    Estimate the identity of LTR sequences in the genome: standard mode
Tue May 21 13:35:26 CST 2024    The identity of LTR sequences: 94.3636850089836%
Tue May 21 13:35:26 CST 2024    Calculate LAI:

                        Done!

Tue May 21 13:35:35 CST 2024    Result file: Vitis_amurensis_ShuangHong_hap2.fasta.mod.out.LAI

                You may use either raw_LAI or LAI for intraspecific comparison
                but please use ONLY LAI for interspecific comparison

Looking forward to your guys' advice!