oushujun
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EDTA Public
Extensive de-novo TE Annotator
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MTEC Public
A repo contains historical and updated MTEC libraries.
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TAIR12-TE Public
A repository to host scripts for annotating TEs in the Arabidopsis TAIR12 (Col-CC) genome
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smapshot Public
Single-molecule accessibility panel snapshots — one annotated read-alignment panel per BED region, with base modifications, nucleosomes, MSPs and FIRE scores over gene and TE tracks
Python UpdatedAug 3, 2026 -
LTR_retriever Public
LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
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LTRRT-Promoter-Suite Public
Forked from cgooden-TE/LTRRT-Promoter-SuiteTools developed to characterize the U3 promoter regions and transcription events of long terminal repeat retrotransposons.
Python UpdatedMay 23, 2026 -
TIR-Learner Public
Forked from KGerhardt/TIR-LearnerTIR-Learner is an ensemble pipeline for Terminal Inverted Repeat (TIR) transposable elements annotation in eukaryotic genomes
Python GNU General Public License v3.0 UpdatedMay 8, 2026 -
AnnoSINE_v2 Public
Forked from KGerhardt/AnnoSINE_v2Accelerating de novo SINE annotation in plant and animal genomes
Python MIT License UpdatedApr 6, 2026 -
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bioconda-recipes Public
Forked from KGerhardt/bioconda-recipesConda recipes for the bioconda channel.
Shell MIT License UpdatedMar 28, 2026 -
LTR_HARVEST_parallel Public
Forked from wild-joker/LTR_HARVEST_parallelAn accessory script to run LTRharvest in parallel modified by @wild-joker.
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LTR_FINDER_parallel Public
A parallel wrapper for LTR_FINDER
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pgr-rice-jbrowse Public
Forked from umgdevelops/ou-jbrowse-genome-dataGenomes with their config files.
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helixer-docker Public
Forked from usadellab/helixer-dockerDockerfile MIT License UpdatedSep 10, 2025 -
TE_consistency Public
A repository to host scripts for calculating TE annotation consistencies
GNU General Public License v3.0 UpdatedAug 21, 2025 -
Maize_TE_Protocol Public
A repository to host scripts created for maize TE annotation protocols
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Citation_Formatter Public
A standalone html for converting .ris, .enw, and .bib citations into formatted list of references.
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riceTElib Public
A collection of manually curated TE examplars in rice (Oryza sativa).
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PopTEvo Public
Study of TE evolution in a population of genomes
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dotPlotly Public
Forked from tpoorten/dotPlotlyGenerate an interactive dot plot from mummer or minimap alignments
HTML MIT License UpdatedJul 22, 2022 -
drosophila-transposons Public
Forked from bergmanlab/drosophila-transposonsDrosophila transposable element canonical sequences
Rich Text Format Creative Commons Zero v1.0 Universal UpdatedJul 11, 2022 -
PodPlot Public
Forked from schatzlab/PodPlotPlot coverage or percent of total sequence as a function of minimum read length
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seqtk Public
Forked from malonge/seqtkToolkit for processing sequences in FASTA/Q formats
C MIT License UpdatedJul 8, 2020 -
Maize_NC358 Public
The repository for codes developed to generated the Maize NC358 assemblies and analyses.
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ThetaPi Public
Nucleotide diversity estimation using population SNP data
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Nchart Public
Forked from MariaNattestad/NchartCreates an N-chart for comparing assembly lengths, including script for counting assembly lengths from a fasta file
R UpdatedFeb 2, 2017