Zhenlisme's Stars
NBISweden/AGAT
Another Gtf/Gff Analysis Toolkit
egluckthaler/starfish
starfish: a modular toolkit for giant mobile element annotation
cgroza/GraffiTE
GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.
mlbendall/telescope
Quantification of transposable element expression using RNA-seq
evotools/nf-LO
A Nextflow workflow to generate lift over files for any pair of genomes
zhangrengang/SubPhaser
Phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.
lh3/miniprot
Align proteins to genomes with splicing and frameshift
qjiangzhao/TEtrimmer
TEtrimmer: a novel tool to automate manual curation of transposable elements
neurogenomics/orthogene
🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖 🔁 🐐 🔁 🐎 🔁 🐈 🔁 🐕 🔁 🐁 🔁 🐒 🔁 🦧 🔁 🦍 🔁 🏃♀️
weng-lab/TEMP2
Algorithm to detect germline and de novo transposon insertions
shohei-kojima/MEGAnE
MEGAnE
hms-dbmi/hic-data-analysis-bootcamp
Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.
elzbth/jitterbug
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.
parklab/xTea
Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
fmenardo/Treemmer
Python tool to reduce size and redundancy of phylogenetic datasets
ablab/quast
Genome assembly evaluation tool
DecodeGenetics/Ratatosk
Hybrid error correction of long reads using colored de Bruijn graphs
vibansal/HapCUT2
software tools for haplotype assembly from sequence data
malonge/RagTag
Tools for fast and flexible genome assembly scaffolding and improvement
malonge/RaGOO
RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
moeinzadeh/Ranbow
zengxiaofei/HapHiC
HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data
IOB-Muenster/denovoTE-eval
Supporting repository for article "Software Evaluation for 'de novo' Detection of Transposons"
inab/trimal
A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0
Zhenlisme/SeqFindpy
This script can be used for searching a sequence in a fasta-format file.
crazyhottommy/RNA-seq-analysis
RNAseq analysis notes from Ming Tang