pirovc

genome_updater. 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.

ganon. ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more

multitax. A Python package for obtaining, parsing and exploring biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)

grimer. GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and metadata with focus on contamination detection.

metameta. Python

dudes. DUDes: a top-down taxonomic profiler for metagenomics and metaproteomics

taxsbp. TaxSBP - Taxonomic structured bin packing implementation

metabench. MetaBench is a pipeline to run and benchmark metagenomics tools. It covers database construction, taxonomic binning and profiling.

fgap. an automated gap closing tool

ganon_benchmark. benchmarking scripts for ganon

metametamerge. Python

pylca. Lowest common ancestor (LCA) algorithm implementation in Python