taxonomy-assignment

There are 24 repositories under taxonomy-assignment topic.

  • widdowquinn/pyani

    Application and Python module for average nucleotide identity analyses of microbes.

    Language:Python2001225655

  • Joseph7e/Assign-Taxonomy-with-BLAST

    Assign taxonomy with blast, can be used for qiime

    Language:Python21577

  • flefler/CyanoSeq

    CyanoSeq: A curated cyanobacterial 16S rRNA database for next-generation sequencing

    15230

  • Grice-Lab/HmmUFOtu

    An HMM and Phylogenetic Placement based Ultra-Fast Taxonomy Assignment Tool for 16S sequencing

    Language:C++116129

  • nf-core/phyloplace

    nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.

    Language:Groovy716043

  • NBISweden/contigtax

    Taxonomic classification of metagenomic contigs

    Language:Python63976

  • Abhinand20/AUTO-ONTO

    Tool to automatically extract keyphrases from text spanning across vast domains, and generate an ontology.

    Language:Jupyter Notebook3101

  • Smithsonian/EPICC-name-match

    Shiny app that matches scientific names to the EPICC taxonomy

    Language:R260

  • appliedbinf/URDO-SMOREd

    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.

    Language:Python13141

  • joonahn/taxqueue

    Taxonomy assignment with task queue

    Language:JavaScript1200

  • linzhi2013/bold_identification

    To identify taxa of given sequences via BOLD system (http://www.boldsystems.org/index.php)

    Language:Python1212

  • marlaux/Metabarcoding-script-by-script

    Former version of METAPIPE

    Language:Shell1100

  • nwnoll/taxalogue

    taxalogue - a toolkit to create comprehensive CO1 reference databases

    Language:Ruby1120
  • MetaTag

    Robaina/MetaTag

    metaTag: functional and taxonomical annotation of metagenomes through phylogenetic tree placement

    Language:Python12700

  • Royal-Botanic-Gardens-Victoria/PAFTOL-taxonomy-classifier

    #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 scripts used below are also in your PATH #Download PAFTOL V2.0 Angio353 genes from Kew #After building the DB, the scripts kraken2paired.py and top_taxa.py can be used to identify taxonomy of unknown samples. #e.g. #kraken2paired.py "reads/*.fastq" kraken_results/ 0 24 kraken2_paftol2/ #top_taxa.py "kraken_results/*" kraken.out

    Language:Python1000

  • Vini2/CheckS

    Checking the presence of a species in a metagenomics sample with known taxonomic composition

    Language:Python110

  • ClemSc/BLAST_2_LCA

    Language:Python0100

  • ebeauchamps/multi-taxonomies

    A Statamic (4.x and 5.x) addon

    Language:PHP0100

  • justin-tpb/TaxIDs-to-SankeyMATIC

    Fetch taxonomic information from Entrez using a list of TaxIDs and visualize user-selected taxonomic ranks with SankeyMATIC.

    Language:Python0100

  • LouisVanLangendonck/UPC-BSG-TaxonomicAssignment

    Find the best taxonomic assignement for the given genomic sequence based on maximum F-measure.

    Language:Python0100

  • lucaTriboli/DiMHepy

    Python module that provide an alternative view of the outputs produced by the software pyani

    Language:Python0010
  • PhyloMAF

    mmtechslv/PhyloMAF

    Next Generation Phylogenetic Microbiome Analysis Framework

    Language:Python0000

  • mmtechslv/taxamatcher

    Correlates target taxonomy(i.e consensus lineages) with a reference taxonomy such as Greengenes, SILVA, etc.

    Language:Python0000

  • trocialba/anvio_metagenomic_workflow

    In this tutorial it is provided an overview of the anvi’o workflow for the analysis of assembly-based shotgun metagenomic data.

    0100