Alessandro Varani's repositories
Plant_Annotation_TEs
Methods and recipes for Plant Genome Annotation - Transposable Elements
JupiterPlot
A Circos-based tool to visualize genome assembly consistency
Plant_Annotation
Plant Genome Annotation Methods and Recipes - Structural Gene Annotation
shinyCircos
an R/shiny application for creation of Circos plot interactively
BLSOM
Batch SOM for Nucleotides
clinker
Gene cluster comparison figure generator
conda
OS-agnostic, system-level binary package manager and ecosystem
dante
Domain based annotation of transposable elements
DupGen_finder
A pipeline used to identify different modes of duplicated gene pairs
EVidenceModeler
source code for EVM
FunGAP
FunGAP: fungal Genome Annotation Pipeline
hic-pipeline
A pipeline for scaffolding a genome assembly using Hi-C
HiC_tools
A collection of tools for Hi-C data analysis
hifiasm
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
jupyterplot
Create real-time plots in Jupyter Notebooks.
MG2C
A user-friendly online tool for drawing genetic maps
MUMandCo
MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation
ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
PASApipeline
PASA software
pgap
NCBI Prokaryotic Genome Annotation Pipeline
prokka
:zap: :aquarius: Rapid prokaryotic genome annotation
pseudohaploid
Create a pseudohaploid assembly from a partially resolved diploid assembly
Scripts_for_GB
The code used in the manuscript titled "Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants".
shinyheatmap
Web application for enormous biological heatmaps
smudgeplot
Inference of ploidy and heterozygosity structure using whole genome sequencing data
synvisio
SynVisio is an interactive multiscale visualization tool that lets you explore the results of McScanX a popular synteny and collinearity detection toolkit.
TBtools
GUI/CommandLine Tool Box for biologistists to utilize NGS data.
tn3-ta_finder
Tn3 Transposon/Toxin Finder