MAG-Explorer-Pipeline is an automated workflow for the recovery, quality assessment, taxonomic classification, and downstream analysis of metagenome-assembled genomes (MAGs) from complex environmental sequencing datasets. The pipeline integrates genome binning, contamination assessment, completeness evaluation, functional annotation, and phylogenomic analyses to facilitate the discovery and characterization of previously uncultured microorganisms. Designed for scalability and reproducibility, MAG-Explorer-Pipeline supports large-scale metagenomic projects aimed at exploring microbial diversity, evolutionary relationships, and the genomic basis of ecological adaptation.
View on GitHubITS-Metagenome-Miner is an automated bioinformatics workflow designed to recover fungal ITS sequences directly from shotgun metagenomic datasets. The pipeline streamlines quality control, ITS extraction, taxonomic assignment, and diversity analyses, enabling efficient characterization of fungal communities from complex environmental and host-associated samples. The workflow facilitates fungal biodiversity studies, microbiome research, and large-scale mining of publicly available metagenomic data.
View on GitHubSRA-Miner is a high-throughput bioinformatics framework developed for large-scale mining of fungal and microbial sequence data from the NCBI Sequence Read Archive (SRA). The workflow automates sequence retrieval, screening, taxonomic identification, and genome discovery from thousands of publicly available datasets. SRA-Miner facilitates the detection of rare taxa, recovery of novel genomes and metagenome-assembled genomes (MAGs), and the exploration of microbial diversity across diverse environments. The pipeline has been applied to identify previously overlooked fungal lineages and expand genomic resources for poorly studied microorganisms.
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