muddy_mine - mining pipeline
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Updated
Nov 27, 2021 - Python
muddy_mine - mining pipeline
Find the best taxonomic assignement for the given genomic sequence based on maximum F-measure.
create RDP classifier training files from NCBI taxonomy gbff file
Python library to deal with taxonomic IDs and lineages from the NCBI's Taxdump files
Ribosomal RNA Allele Tree
Compare which reptile species are available in NCBI's Taxonomy Browser to those in the Reptile Database (RDB).
With Tkinter GUI. Provides autocomplete suggestions for organism names from a SQLite database, using Levenshtein distance for string matching.
NAUniSeq: A fast computational pipeline to search unique sequences for microbial diagnostics
This Python script retrieve all children organism under an ancestor in NCBI taxonomy.
Download genomes from NCBI GenBank FTP site
Python library and command line script , for fast extraction of subtrees of fairly large trees, consisting of millions of nodes, such as the NCBI taxonomy tree.
Assign taxonomy with blast, can be used for qiime
🐣 locally query the ncbi taxonomy
FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )
Add a description, image, and links to the ncbi-taxonomy topic page so that developers can more easily learn about it.
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