PathoGenOmics Lab

All

11 repositories

VIPERA
Public
A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis
bioinformatics snakemake reporting sars-cov-2 virus-evolution intrahost
Python
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GNU General Public License v3.0
•0•6•0•0•Updated Aug 1, 2025Aug 1, 2025
mycolorsTB
Public
R Color package for Mycobacterium tuberculosis complex
r-package tuberculosis mycobacterium-tuberculosis-complex mycobacterium-tuberculosis colors-palette
R
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GNU General Public License v3.0
•0•5•0•0•Updated Aug 1, 2025Aug 1, 2025
transcluster
Public
A Snakemake workflow to find SARS-CoV-2 clusters in a reference phylogeny and estimate their normalized clustering index
bioinformatics snakemake transmission sars-cov-2
Python
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GNU General Public License v3.0
•0•2•0•0•Updated May 2, 2025May 2, 2025
tcfinder
Public
A lightweight tool to find clusters of samples within a phylogeny
rust bioinformatics clustering phylogenetics bioconda clades
Rust
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GNU General Public License v3.0
•0•1•0•0•Updated May 2, 2025May 2, 2025
ena-spike-ntd-repdel-analysis
Public
A Snakemake workflow with associated scripts used for detecting spike NTD repaired deletions in SARS-CoV-2 Omicron BA.1 lineage reads. Manuscript under review.
bioinformatics snakemake pipeline sars-cov-2
Python
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GNU General Public License v3.0
•0•0•0•0•Updated May 2, 2025May 2, 2025
get_MNV
Public
Identifies multiple SNVs within the same codon, reclassifies them as MNVs, and accurately computes resulting amino acid changes from genomic reads
rust annotation vcf snp bam snv mnv
Rust
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GNU General Public License v3.0
•1•6•0•0•Updated Feb 21, 2025Feb 21, 2025
snpick
Public
snpick is a fast and memory-efficient Rust-based SNP extraction tool designed to handle large genomic alignments with minimal RAM usage and high-speed performance.
rust fast snps alignments fasta raxml phylogeny asc iqtree raxml-ng
Rust
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GNU General Public License v3.0
•2•8•0•0•Updated Nov 20, 2024Nov 20, 2024
SARStools
Public
Python
•0•0•0•0•Updated Jul 4, 2024Jul 4, 2024
CrossInfectMTB
Public
Repo for bioinformatic analysis about MTB infections
Shell
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GNU General Public License v3.0
•0•0•0•0•Updated Jun 19, 2024Jun 19, 2024
misb-sysbio-training
Public
Master on Integrative Synthetic Biology (MISB) training sessions
workshop systems-biology jupyter-notebook metabolism cobra cobrapy
Jupyter Notebook
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GNU General Public License v3.0
•0•1•0•0•Updated May 15, 2024May 15, 2024
getNCBImetadata
Public
🪛 Fetch ncbi metadata for sra and assemblies
metadata ncbi genomes sra assemby
Python
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GNU General Public License v3.0
•0•0•0•0•Updated Jan 28, 2024Jan 28, 2024