Vitor C. Piro
Software
§ ganon2 is a k-mer-based classification tool that uses hierarchical interleaved Bloom filters to efficiently classify genomic sequences against large reference sets. It offers integrated database download and updates (RefSeq/GenBank), taxonomic profiling (NCBI/GTDB), binning, hierarchical classification and customised reporting.
§ genome_updater is a bash script that downloads and updates (non-redundant) snapshots of the NCBI Genomes repository (RefSeq/GenBank) with advanced filters, detailed logs and reports, file integrity checks, NCBI taxonomy and GTDB integration and support for parallel downloads.
§ MultiTax is a Python package that provides a standardised set of functions for downloading, parsing, filtering and exploring multiple taxonomies, including GTDB, NCBI, Silva, Greengenes and Open Tree Taxonomy, as well as custom-formatted taxonomies.
§ GRIMER performs analysis of microbiome data and generates a portable and interactive dashboard integrating annotation, taxonomy and metadata with focus on contamination detection.
§ TaxSBP is am implementation of the approximation algorithm for the hierarchically structured bin packing problem based on the NCBI Taxonomy database.
§ MetaMeta is a pipeline to execute and integrate results from metagenome analysis tools. It provides an easy workflow to run multiple tools with multiple samples, producing a single enhanced output profile for each sample.
§ DUDes is a reference-based taxonomic profiler with a top-down approach to analyze metagenomic NGS samples. Instead of using the lowest common ancestor we developed the deepest uncommon descendent.
§ FGAP is an automated gap closing tool. It uses BLAST to align multiple contigs against a draft genome assembly aiming to find sequences that overlap gaps. The algorithm selects the best sequence to fill and eliminate the gap.
§ genome_updater is a bash script that downloads and updates (non-redundant) snapshots of the NCBI Genomes repository (RefSeq/GenBank) with advanced filters, detailed logs and reports, file integrity checks, NCBI taxonomy and GTDB integration and support for parallel downloads.
§ MultiTax is a Python package that provides a standardised set of functions for downloading, parsing, filtering and exploring multiple taxonomies, including GTDB, NCBI, Silva, Greengenes and Open Tree Taxonomy, as well as custom-formatted taxonomies.
§ GRIMER performs analysis of microbiome data and generates a portable and interactive dashboard integrating annotation, taxonomy and metadata with focus on contamination detection.
§ TaxSBP is am implementation of the approximation algorithm for the hierarchically structured bin packing problem based on the NCBI Taxonomy database.
§ MetaMeta is a pipeline to execute and integrate results from metagenome analysis tools. It provides an easy workflow to run multiple tools with multiple samples, producing a single enhanced output profile for each sample.
§ DUDes is a reference-based taxonomic profiler with a top-down approach to analyze metagenomic NGS samples. Instead of using the lowest common ancestor we developed the deepest uncommon descendent.
§ FGAP is an automated gap closing tool. It uses BLAST to align multiple contigs against a draft genome assembly aiming to find sequences that overlap gaps. The algorithm selects the best sequence to fill and eliminate the gap.