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chinese_indicine_pan-genome_project_scripts_and_piplines

Chinese indicine cattle pan-genome project scripts and piplines

circos_pangenome

Calculates overlap of multiple genomes and prepares files for CIRCOS visualization software

deep-hpi-pred

estimate_genome_size.pl

Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish

eupan

EUcaryotic PAN-genome analysis toolkit

get_homologues

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

jcvi

Python utility libraries on genome assembly, annotation and comparative genomics

lorean

Long Reads Annotation pipeline

mungbean_plantcom

Liu C, Wang Y, Peng J, et al. High-quality genome assembly and pan-genome studies facilitate genetic discovery in mung bean and its improvement. Plant Commun. 2022;3(6):100352. doi:10.1016/j.xplc.2022.100352

organelle_pba

A software to assemble chloroplast and mitochodrial genomes using PacBio data

pan-genome-002

Pan-genome methods used by MaizeGDB for the pan-gene tab

pan-genome-analysis

Processing pipeline for pan-genome visulization and exploration

pan_genome

pan_genome_scripts

Python scripts for constructing pangenomes using the iterative mapping style for the Bioinformatics Methods chapter: Making a Pan genome using the iterative mapping approach

pangenome-haplotypes

Scripts to do haplotype analysis on pan genomes.

pgcm

Code related to the manuscript titled "Plant pan-genomes are highly vulnerable to methodological considerations"

rice_ribo-seq

This repository contains some scripts used to analyze Ribo-seq data in rice.

roary

Rapid large-scale prokaryote pan genome analysis

setaria-pan-genome

Here, we de novo assembled 110 representative Setaria accessions from a worldwide collected 1,844 variteies, and performed pan-/graph- genome studies, as well as demographic and genetic studies of Setaria.

tomatosuperpangenome

Here, we sequence and de novo assemble chromosome-scale genomes of nine wild species and two cultivated accessions of tomato and constructed a pan-genome, revealing phylogenetic relationships and structural variation among Lycopersicon