widdowquinn/pyani

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

Language: Python - Size: 185 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 208 - Forks: 57

justin-tpb/TaxIDs-to-SankeyMATIC

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

Language: Python - Size: 109 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

nf-core/phyloplace

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

Language: Nextflow - Size: 3.4 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 10 - Forks: 5

Joseph7e/Assign-Taxonomy-with-BLAST

Assign taxonomy with blast, can be used for qiime

Language: Python - Size: 63.5 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 22 - Forks: 7

rcedgar/viratax

Taxonomy classification of viral sequences / contigs

Language: Python - Size: 5.03 MB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 12 - Forks: 1

Grice-Lab/HmmUFOtu

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

Language: C++ - Size: 53.3 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 11 - Forks: 9

ClemSc/BLAST_2_LCA

Language: Python - Size: 95.7 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

NBISweden/contigtax

Taxonomic classification of metagenomic contigs

Language: Python - Size: 4.26 MB - Last synced at: 3 months ago - Pushed at: 10 months ago - Stars: 6 - Forks: 6

flefler/CyanoSeq

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

Size: 863 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 11 - Forks: 0

nwnoll/taxalogue

taxalogue - a toolkit to create comprehensive CO1 reference databases

Language: Ruby - Size: 882 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

ebeauchamps/multi-taxonomies

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

Language: PHP - Size: 72.3 KB - Last synced at: 11 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

marlaux/Metabarcoding-script-by-script

Former version of METAPIPE

Language: Shell - Size: 12.9 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

linzhi2013/bold_identification

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

Language: Python - Size: 188 KB - Last synced at: 3 days ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 2

Abhinand20/AUTO-ONTO

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

Language: Jupyter Notebook - Size: 1.55 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 1

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: Python - Size: 11.7 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

Vini2/CheckS

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

Language: Python - Size: 222 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

LouisVanLangendonck/UPC-BSG-TaxonomicAssignment

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

Language: Python - Size: 4.88 KB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

Robaina/MetaTag

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

Language: Python - Size: 70.3 MB - Last synced at: about 13 hours ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

Smithsonian/EPICC-name-match 📦

Shiny app that matches scientific names to the EPICC taxonomy

Language: R - Size: 44.9 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 0

mmtechslv/PhyloMAF

Next Generation Phylogenetic Microbiome Analysis Framework

Language: Python - Size: 86.5 MB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

mmtechslv/taxamatcher

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

Language: Python - Size: 15.6 KB - Last synced at: 6 days ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

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: Python - Size: 24.5 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 1

lucaTriboli/DiMHepy

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

Language: Python - Size: 431 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

joonahn/taxqueue

Taxonomy assignment with task queue

Language: JavaScript - Size: 1.4 MB - Last synced at: over 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0