My PhD dissertation on bovine pangenome graph
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Updated
Jul 19, 2021 - TeX
My PhD dissertation on bovine pangenome graph
Single Cell guided Pangenome analysis pipeline using SPAdes, CheckM, GTDB-Tk, Prokka, Roary and extensive quality control.
Repository dedicated to the experiment section of the paper: Revisiting pangenome openness with k-mers. bioRxiv. (2023).
Scripts to analyze the data for the paper "An outstanding bacterial membranome requires CRISPR-Cas systems to avoid the intervention of phages" and derive the figures or subfigures shown in the manuscript.
SCAPE - StaphyloCoccus Aureus Pangenome Exploration
maf to panache and extracting all snps and pangenome specific information.
💻💡💪 D4GEN2023 Hackaton 🧬🏆👨💻
a pacbiohifi read check for the quick view of the read types.
Pangenome clustering using entropy, relative entropy, cumulative RE, hybrid distributions, et.al
Archive of personal scripts repository from my various projects in the Buell Lab at MSU (Jan. 2008 - Apr. 2011)
A repository as a Supplementary Methods of Moulana et al., 2019
Protegenomics analysis based on Pangenome references
Leveraging WES short reads for PAN-EXOME creation and analysis.
sra cloner and interacts with the nucleotide sra and allows for multiple sra fetcher
PAPi (Pangenome Analysis Pipeline)
The lumpy skin disease virus (LSDV) pangenome variation graph (PVG)
estimating proportion of the pangenome across the species post orthology runs.
Analysis of shared parts of a pangenome
a pangraph visualization and pangenome visualization component for the pangenome.
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