Former version of METAPIPE
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Updated
May 9, 2024 - Shell
Former version of METAPIPE
Fetch taxonomic information from Entrez using a list of TaxIDs and visualize user-selected taxonomic ranks with SankeyMATIC.
Application and Python module for average nucleotide identity analyses of microbes.
An HMM and Phylogenetic Placement based Ultra-Fast Taxonomy Assignment Tool for 16S sequencing
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
taxalogue - a toolkit to create comprehensive CO1 reference databases
Assign taxonomy with blast, can be used for qiime
Checking the presence of a species in a metagenomics sample with known taxonomic composition
metaTag: functional and taxonomical annotation of metagenomes through phylogenetic tree placement
CyanoSeq: A curated cyanobacterial 16S rRNA database for next-generation sequencing
Tool to automatically extract keyphrases from text spanning across vast domains, and generate an ontology.
To identify taxa of given sequences via BOLD system (http://www.boldsystems.org/index.php)
Find the best taxonomic assignement for the given genomic sequence based on maximum F-measure.
In this tutorial it is provided an overview of the anvi’o workflow for the analysis of assembly-based shotgun metagenomic data.
Shiny app that matches scientific names to the EPICC taxonomy
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…
Taxonomic classification of metagenomic contigs
Correlates target taxonomy(i.e consensus lineages) with a reference taxonomy such as Greengenes, SILVA, etc.
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.
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