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1. 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 hie…

   Python 106 14

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

   Python 52 5

3. 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…

   Shell 172 18

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

   Python 28 3

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

   Python 8 1

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

   Python 6