RNAseq analysis notes from Ming Tang

Tools for fast and flexible genome assembly scaffolding and improvement

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag

HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data

Earl Grey: A fully automated TE curation and annotation pipeline

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics

TEtrimmer: a novel tool to automate manual curation of transposable elements

Quantification of transposable element expression using RNA-seq

A novel genome assembly pipeline based on deep learning

To phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.

⛓ Correct misassemblies using linked AND long reads

Python tool to reduce size and redundancy of phylogenetic datasets

HiC-Hiker: A probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C

MEGAnE

Jitterbug is a bioinformatic software that predicts insertion sites of transposable elements in a sample sequenced by short paired-end reads with respect to an assembled reference.

An Example of Subgenome Phasing for Complex Allopolyploidy

Supporting repository for article "Software Evaluation for 'de novo' Detection of Transposons"

This script can be used for searching a sequence in a fasta-format file.