Tools & Databases
A collection of bioinformatics tools, pipelines, and interactive genomic databases developed by the TLMR Lab.
Interactive Databases
PiGICo Explorer
This interactive companion to the PiGICo (Pig Gut Integrated Cohort) resource enables high-resolution functional profiling of the swine gut microbiome. It facilitates comparative analyses of taxonomic diversity and metabolic potential, allowing users to query specific functional traits, including antimicrobial resistance determinants, secondary metabolite biosynthetic pathways, and virulence factors, across diverse swine populations.
RuMiDB
Rumen Microbiome Database
Designed for the exploration of the rumen microbial ecosystem, this database offers detailed functional annotations of microbial genomes from bovine sources. It enables the targeted investigation of metabolic redundancy and specialization, providing curated insights into carbohydrate depolymerization machinery, methanogenesis pathways, and the biosynthetic capacity of the rumen microbiota.
Bioinformatics Tools & Pipelines
PiGICo
Pig Gut Integrated Cohort
A comprehensive genomic resource used to characterize the taxonomic breadth and metabolic capacity of swine gut microbes. It annotates key functional traits, including ARGs, virulence factors, and specialized metabolic pathways, and leverages machine learning to associate functional profiles with host health phenotypes.
MAGnet
Modular metagenomic binning framework
A modular, HPC-friendly metagenomic binning and refinement wrapper suite designed to recover high-quality MAGs using ensemble binning and fast consensus refinement. It supports sample grouping for co-assemblies and is optimized for scalability in large-scale metagenomic analyses.
