oushujun

Shujun Ou's repositories

EDTA

Extensive de-novo TE Annotator

Language:PerlGPL-3.0373 9 540

LTR_retriever

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.

Language:PerlGPL-3.0197 6 181

LTR_FINDER_parallel

A parallel wrapper for LTR_FINDER

Language:PerlMIT49 2 11

MTEC

A repo contains historical and updated MTEC libraries.

Language:Perl18 10

PopTEvo

Study of TE evolution in a population of genomes

Language:CGPL-3.09 20

ThetaPi

Nucleotide diversity estimation using population SNP data

Language:Perl6 20

TAIR12-TE

A repository to host scripts for annotating TEs in the Arabidopsis TAIR12 (Col-CC) genome

Language:RGPL-3.04 20

Maize_NC358

The repository for codes developed to generated the Maize NC358 assemblies and analyses.

Language:Jupyter Notebook3 4 1

Maize_TE_Protocol

A repository to host scripts created for maize TE annotation protocols

Language:PerlGPL-3.02 20

riceTElib

A collection of manually curated TE examplars in rice (Oryza sativa).

2 20

Citation_Formatter

A standalone html for converting .ris, .enw, and .bib citations into formatted list of references.

Language:HTMLGPL-3.01 10

PodPlot

Plot coverage or percent of total sequence as a function of minimum read length

Language:Python100

AnnoSINE_v2

SINE annotation tool for plant genomes

Language:PythonMIT000

dotPlotly

Generate an interactive dot plot from mummer or minimap alignments

Language:HTMLMIT000

drosophila-transposons

Drosophila transposable element canonical sequences

Language:Rich Text FormatCC0-1.0000

LTR_HARVEST_parallel

An accessory script to run LTRharvest in parallel modified by @wild-joker.

Language:PerlMIT010

Nchart

Creates an N-chart for comparing assembly lengths, including script for counting assembly lengths from a fasta file

Language:R000

seqtk

Toolkit for processing sequences in FASTA/Q formats

Language:CMIT000