Medium scale identification of genomic neighbors in bacterial genomes
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Updated
May 17, 2024 - Python
Medium scale identification of genomic neighbors in bacterial genomes
genome assembler for cleaning, mapping and assembling genomes.
interpro domain analyzer
interpro to graphs for analyzing domains.
From assemblies to transmission events networks
pangenome metagenomics normalizer for gene annotations specifically gene ontologies.
Pipeline for de novo assembly of bacterial genomes from paired-end Illumina reads
Bacterial plasmid annotation pipeline
Variant barcoding pipeline using single nucleotide polymorphisms (SNPs) for the generation of M. orygis standardised markers for diagnostic and epidemiological use.
A Bash script that automates the search in bacterial genomes for LuxR and LuxI -like proteins. These are important components for Quorum Sensing in bacteria
bacterial genome deep learning using keras
An atlas of high-quality Bacillus cereus group genomes with standardized, manually curated metadata
R approach to analyze evolutionary phylogenomics
HMMER-based microcin search using full microcin sequences and double-glycine signal region.
Bioinformatics
Various scripts I used during my tenure as a Postdoctoral Associate at Cornell University
genome annotation analyzer for the microbiome analysis
Script to design core genome phylogeny using bacterial genome assemblies
from trinity assembly to deep learning.
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