PathoGenOmics Lab
An interdisciplinary research group dedicated to unraveling the complexities of microbial pathogens and their relationships with hosts.
Spain
Pinned Repositories
CrossInfectMTB
Repo for bioinformatic analysis about MTB infections
get_MNV
Identifies multiple SNVs within the same codon, reclassifies them as MNVs, and accurately computes resulting amino acid changes from genomic reads
getNCBImetadata
🪛 Fetch ncbi metadata for sra and assemblies
misb_training_2024
Master on Integrative Synthetic Biology (MISB) training sessions 2024
mycolorsTB
R Color package for Mycobacterium tuberculosis complex
SARStools
snpick
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.
tcfinder
A lightweight tool to find clusters of samples within a phylogeny
transcluster
A Snakemake workflow to find SARS-CoV-2 clusters in a reference phylogeny and estimate their normalized clustering index
VIPERA
A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis
PathoGenOmics Lab's Repositories
PathoGenOmics-Lab/snpick
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.
PathoGenOmics-Lab/get_MNV
Identifies multiple SNVs within the same codon, reclassifies them as MNVs, and accurately computes resulting amino acid changes from genomic reads
PathoGenOmics-Lab/mycolorsTB
R Color package for Mycobacterium tuberculosis complex
PathoGenOmics-Lab/VIPERA
A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis
PathoGenOmics-Lab/transcluster
A Snakemake workflow to find SARS-CoV-2 clusters in a reference phylogeny and estimate their normalized clustering index
PathoGenOmics-Lab/misb_training_2024
Master on Integrative Synthetic Biology (MISB) training sessions 2024
PathoGenOmics-Lab/tcfinder
A lightweight tool to find clusters of samples within a phylogeny
PathoGenOmics-Lab/CrossInfectMTB
Repo for bioinformatic analysis about MTB infections
PathoGenOmics-Lab/ena-spike-ntd-repdel-analysis
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.
PathoGenOmics-Lab/getNCBImetadata
🪛 Fetch ncbi metadata for sra and assemblies
PathoGenOmics-Lab/SARStools