tahirulqamar

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

tahirulqamar/Chinese_indicine_pan-genome_project_scripts_and_piplines

Chinese indicine cattle pan-genome project scripts and piplines

tahirulqamar/CIRCOS_PanGenome

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

tahirulqamar/Deep-HPI-pred

tahirulqamar/estimate_genome_size.pl

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

tahirulqamar/EUPAN

EUcaryotic PAN-genome analysis toolkit

tahirulqamar/get_homologues

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

tahirulqamar/jcvi

Python utility libraries on genome assembly, annotation and comparative genomics

tahirulqamar/LoReAn

Long Reads Annotation pipeline

tahirulqamar/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

tahirulqamar/Organelle_PBA

A software to assemble chloroplast and mitochodrial genomes using PacBio data

tahirulqamar/Pan-Genome-002

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

tahirulqamar/pan-genome-analysis

Processing pipeline for pan-genome visulization and exploration

tahirulqamar/pan_genome

tahirulqamar/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

tahirulqamar/pangenome-haplotypes

Scripts to do haplotype analysis on pan genomes.

tahirulqamar/PGCM

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

tahirulqamar/Rice_Ribo-seq

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

tahirulqamar/Roary

Rapid large-scale prokaryote pan genome analysis

tahirulqamar/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.

tahirulqamar/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

tahirulqamar/VirtuDockDL