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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Updated
May 17, 2022
In this tutorial it is provided an overview of the anvi’o workflow for the analysis of assembly-based shotgun metagenomic data.
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…
Shiny app that matches scientific names to the EPICC taxonomy
Find the best taxonomic assignement for the given genomic sequence based on maximum F-measure.
taxalogue - a toolkit to create comprehensive CO1 reference databases
Taxonomy assignment with task queue
metaTag: functional and taxonomical annotation of metagenomes through phylogenetic tree placement
Former version of METAPIPE
Checking the presence of a species in a metagenomics sample with known taxonomic composition
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.
CyanoSeq: A curated cyanobacterial 16S rRNA database for next-generation sequencing
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.
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)
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
Taxonomic classification of metagenomic contigs
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