metagenomics visualization library

Web page for assigning taxonomy of microorganisms.

Create BIOM-format tables (https://biom-format.org) from CLARK output (https://clark.cs.ucr.edu/) for use with downstream tools such as UniFrac, iTol (itol.embl.de), or PhyloToAST (phylotoast.org), PhyloToAST (https://phylotoast.org).

process raw reads from ubiome

create RDP classifier training files from NCBI taxonomy gbff file

Web application for batch updates of amphibian taxonomies.

Awesome research paper on taxonomy (information retrieval). Study notes about their contributions, methods, and results.

MetaShot (Metagenomics Shotgun) is a complete pipeline designed for the taxonomic classification of the human microbiota members. In MetaShot, third party tools and new developed Python and Bash scripts are integrated to analyze paired-end (PE) Illumina sequences, offering an automated procedure covering all the analysis steps from raw data mana…

Built as a solution to HumAIn, 2019 by TCS.

Taxonomic classification and read binning of mitochondrial DNA

[Features extraction method] You can find the new version of CASTOR_KRFE at https://github.com/bioinfoUQAM/CASTOR_KRFE

Improving data quality of taxonomic assignments in large-scale public databases

Sondovač is a script to create orthologous low-copy nuclear probes from transcriptome and genome skim data for target enrichment. For latest version check "releases".

Evaluation of Statistical Linear Models for Genome Virus Classification

Correlates target taxonomy(i.e consensus lineages) with a reference taxonomy such as Greengenes, SILVA, etc.

Processing modules of the metagenomic visualization tool, MetaG.

The standards proposed by Omni Species for better intercommunicability between the different Biological Systematics platforms.

PyTorch implementation of Metric-Guided Prototype Learning for hierarchical classification.

A script to check fungus names for the most up to date nomenclature according to Species Fungorum 🍄

This library provides a way to parse, manipulate and analyze ICB and GICS Codes.