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LTR_retriever is a command line program (in Perl) for accurate identification of LTR retrotransposons (LTR-RTs) from outputs of LTRharvest, LTR_FINDER, MGEScan 3.0.0, LTR_STRUC, and LtrDetector, and generates non-redundant LTR-RT library for genome annotations.

By default, the program will generate whole-genome LTR-RT annotation and the LTR Assembly Index (LAI) for evaluations of the assembly continuity of the input genome. Users can also run LAI separately (see Usage).

You may use conda to quickly install all dependencies and LTR_retriever is then good to go:

conda create -n LTR_retriever
conda activate LTR_retriever
conda install -y -c conda-forge perl perl-text-soundex
conda install -y -c bioconda cd-hit repeatmasker
git clone https://github.com/oushujun/LTR_retriever.git
./LTR_retriever/LTR_retriever -h

Note: if you experience RepeatMasker errors, you may want to read #43 to fix the library bug.

For the standard installation, you need to provide the paths to the following dependent programs.

1. makeblastdb, blastn, and blastx in the BLAST+ package (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/),
2. cd-hit-est in the CDHIT package (http://weizhongli-lab.org/cd-hit/) OR blastclust in the BLAST package (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.25/),
3. hmmsearch in the HMMER package (http://hmmer.org/; v3.1b2 or higher), and
4. RepeatMasker (http://www.repeatmasker.org/).

Simply modify the 'paths' file in the LTR_retriever directory

vi /your_path_to/LTR_retriever/paths

Then modify lines below:

BLAST+=/your_path_to/BLAST+2.2.30/bin/
RepeatMasker=/your_path_to/RepeatMasker4.0.0/
HMMER=/your_path_to/HMMER3.1b2/bin/
CDHIT=/your_path_to/CDHIT4.6.1/
BLAST=/your_path_to/BLAST2.2.26/bin/ #not required if CDHIT provided

Two types of inputs are needed for LTR_retriever

1. Genomic sequence
2. LTR-RT candidates

LTR_retriever takes multiple LTR-RT candidate inputs including the screen output of LTRharvest and the screen output of LTR_FINDER. For outputs of other LTR identification programs, you may convert them to LTRharvest-like format and feed them to LTR_retriever (with -inharvest). Users need to obtain the input file(s) from the aforementioned programs before running LTR_retriever. Either a single input source or a combination of multiple inputs are acceptable. For more details and examples please see the manual.

It's sufficient and recommended to just provide LTR_retriever with LTRharvest and LTR_FINDER results. However, if you want to analyze results from LTR_STRUC, MGEScan 3.0.0, and LtrDetector, you can use the following scripts to convert their outputs to the LTRharvest format, then feed LTR_retriever with -inharvest. You may concatenate multiple LTRharvest format inputs into one file. For instructions, run:

perl /your_path_to/LTR_retriever/bin/convert_ltr_struc.pl
perl /your_path_to/LTR_retriever/bin/convert_MGEScan3.0.pl
perl /your_path_to/LTR_retriever/bin/convert_ltrdetector.pl

Click to download executables for LTR_FINDER_parallel and LTRharvest. For recommended parameters, please read the Manual.

The output of LTR_retriever includes:

1. Intact LTR-RTs with coordinate and structural information
   • Summary tables (.pass.list)
   • GFF3 format output (.pass.list.gff3)
2. LTR-RT library
   • All non-redundant LTR-RTs (.LTRlib.fa)
   • All non-TGCA LTR-RTs (.nmtf.LTRlib.fa)
   • All LTR-RTs with redundancy (.LTRlib.redundant.fa)
3. Whole-genome LTR-RT annotation by the non-redundant library
   • GFF format output (.out.gff)
   • LTR family summary (.out.fam.size.list)
   • LTR superfamily summary (.out.superfam.size.list)
   • LTR distribution on each chromosome (.out.LTR.distribution.txt)
4. LTR Assembly Index (.out.LAI)

Good practice: It's highly recommended to use short and simple sequence names. For example, use letters, numbers, and _ to generate unique names shorter than 15 bits.

To obtain raw input files with LTRharvest and LTR_FINDER_parallel:

/your_path_to/gt suffixerator -db genome.fa -indexname genome.fa -tis -suf -lcp -des -ssp -sds -dna
/your_path_to/gt ltrharvest -index genome.fa -minlenltr 100 -maxlenltr 7000 -mintsd 4 -maxtsd 6 -motif TGCA -motifmis 1 -similar 85 -vic 10 -seed 20 -seqids yes > genome.fa.harvest.scn
/your_path_to/LTR_FINDER_parallel -seq genome.fa -threads 10 -harvest_out -size 1000000 -time 300
cat genome.fa.harvest.scn genome.fa.finder.combine.scn > genome.fa.rawLTR.scn

To run LTR_retriever:

/your_path_to/LTR_retriever -genome genome.fa -inharvest genome.fa.rawLTR.scn -threads 10 [options]

To run LAI:

/your_path_to/LAI -genome genome.fa -intact genome.fa.pass.list -all genome.fa.out [options]

For more details about the usage and parameter settings, please see the help pages by running:

/your_path_to/LTR_retriever -h

/your_path_to/LAI -h

Or refer to the manual document.

For questions and Issues Please See: https://github.com/oushujun/LTR_retriever/issues

If you find LTR_retriever useful, please cite:

Ou S. and Jiang N. (2018). LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons. Plant Physiol. 176(2): 1410-1422.

If you find LAI useful, 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