MegaLTR is a robust online server and local standalone that can identifies intact LTR-RTs and calculate LTR Assembly Index (LAI) in any target genome. MegaLTR is freely available at https://bioinformatics.um6p.ma/MegaLTR
MegaLTR is a pipeline that detects intact LTR-RTs at the whole genome level. The pipeline integrates the structure-based, homology-based and de novo intact LTR-RT identification, classification, annotation and visualization tools such as LTR_FINEDR, LTRharvest, LTR_retriever, RepeatMasker, CDHIT package, BLAST+ package, HMMER package, LTRdigest, TEsorter, l REANNOTATE, ClustalW, faidx, Rscript, and RIdeogram.
MegaLTR running with three options:
1: Intact LTR-RT identification and annotation of internal domains.
2: Intact LTR-RT Identification and annotation of internal domains plus determination of insertion time.
3: Intact LTR-RT Identification, annotation of internal domains, determination of insertion time, LTR-RT gene-chimera analysis and visualization of gene density and LTR-RTs across chromosomes.
4: LTR Assembly Index (LAI) calculation.
MegaLTR has been tested on Ubuntu 18.04 and 20.04.
- Install
- Required data
- Usage
- Run Example
- Output files
- Output files example
The installation require conda. You can install all dependencies for running MegaLTR in a new conda environment using the MegaLTR.yml file. If you do not have conda, please follow this tutorial.
1- Download repository from github
git clone https://github.com/MoradMMokhtar/MegaLTR.git
2- Go to the MegaLTR folder
cd MegaLTR
3- Create the MegaLTR environment with all dependencies
conda env create -f MegaLTR.yml
4- Activate the MegaLTR environment
conda activate MegaLTR
| Data | Option 1 | Option 2 | Option 3 | Option 4 |
|---|---|---|---|---|
| Genome sequence - Fasta file with chromosomes/scaffolds/contigs sequences | Required | Required | Required | Required |
| Genome annotation - GFF/GFF3 file with genome annotations (gene,CDS,mRNA) | Not Required | Not Required | Required | Not Required |
Go to the MegaLTR folder
bash MegaLTR.sh -A [1 or 2 or 3 or 4] -F [Genome in FASTA Format] -G [GFF/GFF3 File]
#Required arguments:
-A The analysis type [1 or 2 or 3]
1 (for Intact LTR-RT identification and annotation of internal domains 'This analysis needs FASTA file only')
2 (for Intact LTR-RT Identification and annotation of internal domains plus determination of insertion time 'This analysis needs FASTA file only')
3 (for Intact LTR-RT Identification, annotation of internal domains, determination of insertion time, LTR-RT gene-chimera analysis and visualization of gene density and LTR-RTs across chromosomes 'This analysis needs FASTA and GFF files')
4 (for calculate LTR Assembly Index (LAI)'This analysis needs FASTA file only')
-F Your path to the genome sequence (Fasta file).
-G Your path to the genome annotation (GFF/GFF3 file). Required with argument -A 3 only.
#Optional arguments:
-T tRNA sequence file (Locate the filename from the tRNA folder or provide your own tRNA sequence in FASTA format, default is Arabidopsis_thaliana_trna.fa)."
-P Outfileprefix, default is results."
-l Min length of 5'&3'LTR, default is 100."
-L Max length of 5'&3'LTR, default is 7000."
-d Min distance between 5'&3'LTR, default is 1000."
-D Max distance between 5'&3'LTR, default is 15000."
-S Specify similaritythreshold, default is 85."
-M Min length of exact match pair, default is 20."
-B TE Database that TEsorter will use it {gydb,rexdb,rexdb-plant,rexdb-metazoa,sine}, default is rexdb."
-C Mininum coverage for protein domains in HMMScan output, default is 20."
-V Maxinum E-value for protein domains in HMMScan output, default is 0.001."
-Q Classifying rule [identity-coverage-length] based on similarity, default is 80-80-80]."
-E Hmm-database that TEsorter will use it {gydb,rexdb,rexdb-plant,rexdb-metazoa,sine}, default is rexdb]."
-R Neutral mutation rate of the target species (per bp per ya), e.g., rice: 1.3e-8 [0.000000013]; mammal: 2.2e-9 [0.0000000022]; Drosophila: 1.6e-8 [0.000000016], default is 0.000000013."
-U The distance upstream LTR retrotransposons, default is 5000."
-X The distance downstream LTR retrotransposons, default is 5000."
-W Window size to extract gene density from the GFF file, default is 1000000."
-N Number of chromosomes specified in FASTA file to visualize density of genes and LTRs, default is 12."
-v Print MegaLTR version and exit."
-t Indicate how many CPU/threads you want to run MegaLTR, default is 4."
-h Print this Help
Default parameters:bash MegaLTR.sh -A 3 -F /path/to/genome_fasta_file -G /path/to/gff_file -T Arabidopsis_thaliana_trna.fa -P Results -l 100 -L 7000 -d 1000 -D 15000 -S 85 -M 20 -B rexdb -C 20 -V 0.001 -Q 80-80-80 -E rexdb -R 0.000000015 -U 500 -X 5000 -W 1000000 -N 9 -t 6
bash MegaLTR_Run_Example.sh -A 3 -F NC_003070.9_Arabidopsis_thaliana.fna.gz -G Arabidopsis_thaliana.gff.gz
We have collected the main output files in the Collected _Files folder in the main output directory. The results are presented in the form of tables and images as follows:
| # | File name | Description |
|---|---|---|
| 1 | *.fna.pass.list | All LTR-RTs that passed the filtering step |
| 2 | *.fna.nmtf.pass.list | Non-TGCA LTR-RTs that passed the filtering step |
| 3 | *.fna.pass.list.gff3 | GFF3 format for intact LTR-RTs |
| 4 | *.statistics.tsv | LTR family summary |
| 5 | genes_up_and_down_LTR.tsv | Genes up- and down-stream of LTR-RT elements |
| 6 | LTR_Table_Digest_TEsorter _Time_nongene_and_gene.tsv | combine the results of LTR-Finder, LTRharvest, LTR-retriever, LTRdigest, TEsorter, insertion time, LTR-RT-gene chimeras, and LTR-RT near genes in one file |
| 7 | LTR_Table_TEsorter_Digest.tsv | Mergeing of LTR_retriever, LTRdigest, and TEsorter results in one file |
| 8 | *.Digest_TEsorter_Time.tsv | Mergeing of LTR_retriever, LTRdigest, TEsorter, and insertion time results in one file |
| 9 | Gene density and LTR-RTs distribution.png | visualization of gene density and LTR-RTs across chromosomes PNG format |
| 10 | *.length.ids2.Length_boxplot.png | the boxplot of LTR-RT length for both LTR-RTs superfamilies |
| 11 | *.length.ids2.Length_chart.png | statistical distribution of LTR-RT length for both LTR-RTs superfamilies |
| 12 | *.length.ids2.TimeK_boxplot.png | the boxplot of LTR-RT insertion age for both LTR-RTs superfamilies |
| 13 | *.length.ids2.TimeK_chart.png | statistical distribution of LTR-RT insertion age for both LTR-RTs superfamilies |
| 14 | *.length.ids.Length_boxplot.png | the boxplot of LTR-RT length for each LTR-RTs superfamily |
| 15 | *.length.ids.Length_chart.png | statistical distribution of LTR-RT length for each LTR-RTs superfamily |
| 16 | *.length.ids.TimeK_boxplot.png | the boxplot of LTR-RT insertion age for each LTR-RTs superfamily |
| 17 | *.length.ids.TimeK_chart.png | statistical distribution of LTR-RT insertion age for each LTR-RTs superfamily |
| 18 | *.PBS.Sequence.fa | All PBS in FASTA format |
| 19 | *.PPT.Sequence.fa | All PPT in FASTA format |
| 20 | LTR-RT_Sequence.fa | All intact LTR-RTs in FASTA format |
| 21 | .out.LAI | LTR Assembly Index (LAI) value |
- Genes and LTR-RTs density across chromosomes
- Boxplot of LTR-RTs length for all LTR-RTs
- Statistical distribution of LTR-RTs length for all LTR-RTs
- Boxplot of LTR-RTs insertion age for all LTR-RTs
- Statistical distribution of LTR-RTs insertion age for all LTR-RTs
- Boxplot of LTR-RT length for each LTR-RTs class
- Statistical distribution of LTR-RT length for each LTR-RTs class
- Boxplot of LTR-RTs insertion age for each LTR-RTs class
- Statistical distribution of LTR-RTs insertion age for each LTR-RTs class
To report bugs and give us suggestions, you can open an issue here. You may also contact us by e-mail morad.mokhtar@um6p.ma or achraf.elallali@um6p.ma
If you used MegaLTR to calculate LTR Assembly Index (LAI) please cite PlantLAI (https://doi.org/10.1093/aobpla/plad015) and MegaLTR (https://doi.org/10.3389/fpls.2023.1237426) otherwise please cite MegaLTR (https://doi.org/10.3389/fpls.2023.1237426) and PltRNAdb (https://doi.org/10.1371/journal.pone.0268904)