Application and Python module for average nucleotide identity analyses of microbes.
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Oct 16, 2024 - Python
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taxonomy-assignment
Here are 24 public repositories matching this topic...
Assign taxonomy with blast, can be used for qiime
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Aug 18, 2023 - Python
CyanoSeq: A curated cyanobacterial 16S rRNA database for next-generation sequencing
metabarcoding taxonomy-assignment taxonomic-classification amplicon-datasets amplicon-sequencing cyanobacteria taxonomy-database
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Oct 9, 2024
An HMM and Phylogenetic Placement based Ultra-Fast Taxonomy Assignment Tool for 16S sequencing
hmm phylogenetics mixture-model dirichlet-process-mixtures taxonomy-assignment otu phylogenetic-placement jplace
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Dec 2, 2024 - C++
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
workflow pipeline nextflow evolution phylogenetics sequence-classification taxonomy-assignment phylogenetic-placement nf-core evolutionary-tree
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Dec 20, 2024 - Groovy
Taxonomic classification of metagenomic contigs
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Sep 3, 2024 - Python
Shiny app that matches scientific names to the EPICC taxonomy
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May 9, 2022 - R
Tool to automatically extract keyphrases from text spanning across vast domains, and generate an ontology.
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Mar 13, 2023 - Jupyter Notebook
#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…
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Mar 29, 2022 - Python
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.
bioinformatics genomics ngs public-health microbial-genomics bacteria taxonomy-assignment ngs-analysis pathogen-detection
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Mar 24, 2020 - Python
taxalogue - a toolkit to create comprehensive CO1 reference databases
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Aug 5, 2024 - Ruby
Taxonomy assignment with task queue
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Mar 2, 2019 - JavaScript
metaTag: functional and taxonomical annotation of metagenomes through phylogenetic tree placement
bioinformatics metagenomics evolutionary-placement taxonomy-assignment microbial-ecology metagenomics-toolkit marine-microbiology function-annotation
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May 19, 2023 - Python
Former version of METAPIPE
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May 9, 2024 - Shell
Checking the presence of a species in a metagenomics sample with known taxonomic composition
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Aug 18, 2023 - Python
To identify taxa of given sequences via BOLD system (http://www.boldsystems.org/index.php)
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Feb 17, 2023 - Python
In this tutorial it is provided an overview of the anvi’o workflow for the analysis of assembly-based shotgun metagenomic data.
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May 17, 2022
Correlates target taxonomy(i.e consensus lineages) with a reference taxonomy such as Greengenes, SILVA, etc.
bioinformatics taxonomy metagenomics lineage taxonomy-assignment silva taxonomic-classification taxon taxa greengenes
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Mar 16, 2021 - Python
Next Generation Phylogenetic Microbiome Analysis Framework
bioinformatics taxonomy phylogenetic-trees phylogenetics microbiome ott taxonomy-assignment silva microbiome-analysis taxonomic-classification otu-table greengenes 16s-rrna
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Apr 23, 2022 - Python
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Nov 15, 2024 - Python
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