cdLTR_FINDER_parallel-1.1perlLTR_FINDER_parallel LTR_FINDER_parallel使用方法: perl LTR_FINDER_parallel -seq ${genome} -threads 36 -harvest_out #输出是${genome}.finder.combine.scn genomefile="`basename ${genome}`" mv ${genomefile}.finder.combine.scn ${species}.finder.scn 当使用conda时候,可...
conda install-c bioconda/label/cf201901 repeatmasker git clone https://github.com/oushujun/LTR_retriever.git./LTR_retriever/LTR_retriever-h 此外你还需要额外安装LTRharvest,LTR_FINDER和MGEScan_LTR。 LTRharverst:http://genometools.org/ LTR_FINDER:https://github.com/xzhub/LTR_Finder 修改版MGEScan_...
/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 -...
Quick installation using conda Standard installation Inputs Outputs Usage Citations Introduction 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 ge...
LTR_FINDER_parallel gt seqkit LTR_retriever R ggplot2 packages (for visualization only) 1. Install LTR_retriever by conda 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 clo...
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...