code repo for mobileOG-db

• UpdatedJan 23, 2025
• Python

Repository for the TRANSIT and TPP tools developed by the Ioerger Lab

• UpdatedFeb 7, 2025
• Python

This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.

• UpdatedMay 16, 2023
• F*

This repository contains the code for the transposonmapper package to map the transposons from the SATAY sequencing data.

• UpdatedOct 26, 2022
• Jupyter Notebook

transposon insertion site identified from raw fastq file and transposon sequences, using local alignment for identification.

• UpdatedJul 4, 2022

Snakemake pipeline to analyze the integration patterns of the synthetic transposon Sleeping Beauty in relation to several genomic features.

• UpdatedFeb 24, 2022
• Python

Transposable Element Subfamily Detection

• UpdatedJul 30, 2024
• C

Identification of transposon insertion sites

• UpdatedJul 30, 2024
• C++

Methods for detection of horizontal transfer of transposable elements from genome sequences. GPL version 3 license.

• UpdatedApr 19, 2022
• R

A simple bash pipeline for extension and edge polishing of transposable elements consensi.

• UpdatedMay 18, 2022
• Shell

Detect ALU insertions supported by specific split read pairs.

• UpdatedOct 15, 2023
• Shell

A tool for detecting TE insertions and evaluating the insertion rate (under development).

• UpdatedOct 15, 2023
• Python

A few scripts I'm using for transposon analysis

• UpdatedOct 5, 2019
• R

De novo repeat inference from long reads

• UpdatedJul 21, 2021
• Java

TE Annotation code for W85 (diploid blueberry) genome.

• UpdatedMay 27, 2021
• Shell

Transcriptome sequencing assembly

• UpdatedJul 28, 2024
• C++