Application and Python module for average nucleotide identity analyses of microbes.
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Updated
Apr 8, 2024 - Python
Application and Python module for average nucleotide identity analyses of microbes.
Assign taxonomy with blast, can be used for qiime
Taxonomic classification of metagenomic contigs
To identify taxa of given sequences via BOLD system (http://www.boldsystems.org/index.php)
Sequence Matching fOr REpiratory Diseases, SMORE'D, is a command-line sequence classification tool tailored to meet the needs of the Undiagnosed Respiratory Disease Outbreak (URDO) branch at CDC. SMORE'D is a k-mer based classification tool capable of rapidly classifying read sequences generated by multi-pathogen detection platforms.
Correlates target taxonomy(i.e consensus lineages) with a reference taxonomy such as Greengenes, SILVA, etc.
Next Generation Phylogenetic Microbiome Analysis Framework
#Scripts to create Kraken2 database of PAFTOL V2.0 Angio353 genes. An excellent database for taxonomic identification of plants. #https://treeoflife.kew.org/ #https://github.com/DerrickWood/kraken2/wiki #Prior to using this script, download and install kraken2 and make sure it is working and in your PATH. #Make sure the location of the python sc…
metaTag: functional and taxonomical annotation of metagenomes through phylogenetic tree placement
Find the best taxonomic assignement for the given genomic sequence based on maximum F-measure.
Python module that provide an alternative view of the outputs produced by the software pyani
Fetch taxonomic information from Entrez using a list of TaxIDs and visualize user-selected taxonomic ranks with SankeyMATIC.
Checking the presence of a species in a metagenomics sample with known taxonomic composition
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