sjteresi / TE_DensityLinks
Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4
☆33Updated 8 months ago
Alternatives and similar repositories for TE_Density
Users that are interested in TE_Density are comparing it to the libraries listed below
Sorting:
- A python script for finding telomeric repeats (TTAGGG/CCCTAA) in FASTA files☆34Updated 3 years ago
- A genome assembly assessment pipeline.☆37Updated last year
- Accompanying repository for our publications on manual curation methods for Transposable Elements.☆20Updated last year
- ☆30Updated 5 months ago
- ☆40Updated 2 years ago
- ☆32Updated 9 months ago
- ☆20Updated 10 months ago
- A shiny application to visualize MCscan result☆36Updated 2 years ago
- use long sequenced reads to close gaps in assemblies☆37Updated 6 years ago
- scripts for the project of seven thaliana genomes assembly☆39Updated 4 years ago
- Pan-genome Construction and Population Structure Variation Calling pipeline☆41Updated 9 months ago
- Plant genome assembly and annotation pipeline using snakemake☆44Updated last month
- A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats☆66Updated 4 years ago
- ☆25Updated 3 years ago
- Automated pipeline for running CoalHMM☆13Updated last year
- ☆30Updated 3 months ago
- Genome Annotation Pipeline☆36Updated 10 months ago
- Dynamic Elongation of a Genome Assembly Path☆21Updated last year
- C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on Pore-C, HiFi-C/CiFi or Hi-C.☆37Updated last week
- A quick user guide for de novo transposable element (TE) library generation and TE screening. Utilising; the Extensive de novo TE Annotat…☆27Updated 2 years ago
- ☆28Updated 2 years ago
- HiCAT new project☆28Updated last month
- A fast tool for detecting and decomposing segmental duplications in genome assemblies☆48Updated last year
- Scripts that used in our chicken T2T manuscript.☆20Updated last year
- Gene model transfer from closely related reference genomes using cDNA alignments☆10Updated 4 years ago
- ☆28Updated last year
- This repository contains relevant code and explanation for ”Leveraging a phased pangenome to design ideal haplotypes for hybrid potato br…☆30Updated 5 months ago
- TGS scaffolding☆46Updated 3 years ago
- wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication☆34Updated 4 months ago
- scripts☆16Updated 6 years ago