taxonomic-classification

There are 3 repositories under taxonomic-classification topic.

• sourmash

  sourmash-bio / sourmash

  Quickly search, compare, and analyze genomic and metagenomic data sets.

  minhashbioinformaticsrustpythonsourmashfracminhashscaled-minhashkmersketchingtaxonomic-classificationtaxonomic-profilinghacktoberfest
  Language:Python 432

• bioinformatics-centre / kaiju

  Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

  metagenomicsnext-generation-sequencingbioinformaticstaxonomic-classificationtaxonomy
  Language:C 249
• kmcp

  shenwei356 / kmcp

  Accurate metagenomic profiling && Fast large-scale sequence/genome searching

  kmersketchsearchingmetagenomicstaxonomic-classificationtaxonomic-profilingscaled-minhashsyncmerscobssketchingbigsifracminhashvirome
  Language:Go 170

• nf-core / ampliseq

  Amplicon sequencing analysis workflow using DADA2 and QIIME2

  amplicon-sequencing16snf-corenextflowpipelineworkflowmetagenomicsrrna18sitsmetabarcodingqiime2ednataxonomic-classificationilluminaiontorrentmicrobiomepacbiotaxonomic-profiling
  Language:Nextflow 156

• bluenote-1577 / sylph

  ultrafast genome querying and taxonomic profiling for metagenomic samples by abundance-corrected minhash.

  average-nucleotide-identityk-mermetagenomicssketching-algorithmtaxonomic-classification
  Language:Rust 93

• nf-core / taxprofiler

  Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

  bioinformaticsclassificationilluminalong-readsmetagenomicsmicrobiomenanoporenextflownf-corepathogenpipelineprofilingshotguntaxonomic-classificationtaxonomic-profilingworkflow
  Language:Nextflow 90

• pierrebarbera / epa-ng

  Massively parallel phylogenetic placement of genetic sequences

  phylogeneticsbioinformaticstaxonomic-classificationmpiopenmpmpi-ioplacement
  Language:C++ 66

• FOI-Bioinformatics / flextaxd

  FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )

  ncbi-taxonomygtdbganonkraken2custom-taxonomymetagenomic-classificationcustom-databasetaxonomic-classificationtaxonomic-classificationscentrifugekrakenuniqncbi-databaseamplicon16s
  Language:Python 63

• steineggerlab / Metabuli

  Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

  bioinformaticsk-mermetagenomicstaxonomic-classificationtaxonomy
  Language:C++ 62

• smdabdoub / kraken-biom

  Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).

  metagenomicstaxonomytaxonomic-classificationbioinformaticskrakenbiom-format
  Language:Python 44

• laowantong / paroxython

  Tag and recommend Python exercises based on algorithmic features

  algorithmic-featuresalgorithms-and-data-structureseducationknowledge-managementmetaprogrammingpythonstatic-analysistaxonomic-classification
  Language:Python 33

• VSainteuf / metric-guided-prototypes-pytorch

  PyTorch implementation of Metric-Guided Prototype Learning for hierarchical classification.

  deep-learningdeeplearningmachine-learningmachinelearningpytorchclassificationclassification-algorithimshierarchicalhierarchical-modelstaxonomytaxonomic-classification
  Language:Jupyter Notebook 26

• millanp95 / DeLUCS

  This repository contains all the source files required to run DeLUCS, a deep learning clustering algorithm for DNA sequences.

  sequence-clusteringtaxonomic-classificationdeep-learning
  Language:Python 23

• JensUweUlrich / Taxor

  Fast and space-efficient taxonomic classification of long reads

  kmerlong-readlong-read-sequencingmetagenomicssyncmertaxonomic-classificationtaxonomic-profilingbioinfem-algorithmpseudo-alignmentxor-filterinterleaved-xor-filterbioinformaticsmicrobiomerefseqtaxonomy
  Language:C++ 15

• microUCPH / amplicon_data_analysis

  Collection of notebooks describing the basic analysis workflow for a 16S rRNA gene amplicon sequencing project

  microbiomeamplicon-data-analysis16sstatisticsdada2taxonomic-classificationdata-analysis
  Language:HTML 11

• phylo42 / PEWO

  Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees

  placementphylogenetic-placementmetagenomicsmetabarcodingbenchmarkingsnakemakeworkflowphylo-kmerstaxonomic-classification
  Language:Python 11

• bioinfoUQAM / CASTOR_KRFE

  Alignment-free method to identify and analyse discriminant genomic subsequences within pathogen sequences

  rfetaxonomic-classificationvirus-classificationkmersalignment-freecastorfeature-extractionmachine-learningcastor-krfesvmsvm-rfe
  Language:Python 9

• phylo42 / RAPPAS

  Rapid, Alignment-free, Phylogenetic Placement via Ancestral Sequences

  placementphylogenetic-placementmetagenomicsmetabarcodingphylogeneticsgenetic-markerskmersphylo-kmerstaxonomic-classification
  Language:Java 9

• Rekyt / taxo_harmonization

  :notebook: Companion code for Grenié et al. 2022 MEE "Harmonizing taxon names in biodiversity data: a review of tools, databases, and best practices" preprint: 10.32942/osf.io/e3qnz

  taxonomytaxonomic-classificationtaxonomy-databasebiodiversity-databasetaxonomic-databases
  Language:R 9

• ali-kishk / AmpliconNet

  Sequence based 16S rRNA Taxonomic classifier using MLP

  bioinformaticstaxonomic-classification16s-rrnamultilayer-perceptrondeep-learning
  Language:Jupyter Notebook 8

• flefler / CyanoSeq

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

  amplicon-datasetsamplicon-sequencingcyanobacteriametabarcodingtaxonomic-classificationtaxonomy-assignmenttaxonomy-database
  8

• mbhall88 / classification_benchmark

  Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification

  bioinformaticscontaminationsequence-analysistaxonomic-classificationtuberculosis
  Language:Python 8

• peterk87 / filter_classified_reads

  Filter for reads from taxa of interest using Kraken2/Centrifuge classification results.

  bioinformatics-scriptsdna-sequencesfilteringtaxonomic-classification
  Language:Python 7

• earizon / txt_world_domination

  Static site generator "Databaseless" CMS: Content is just (git friendly) markdown with multidimensional topic/tags/taxonomy extensions that both humans and AI will appreciate.

  cmsdocumentationheadless-cmslow-codemarkdownmlstatic-site-generatortaxonomic-classificationtxt
  Language:JavaScript 6

• HKU-BAL / MegaPath

  MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data; MegaPath-Amplicon: filtering module for metagenomic amplicon data

  ngsmetagenomicstaxonomic-classificationampliconfilter
  Language:Java 6

• sourcemeta / json-taxonomy

  A formal taxonomy to classify JSON documents based on their size, type of content, characteristics of their structure and redundancy criteria.

  jsonjson-documenttaxonomic-classificationtaxonomy
  Language:JavaScript 6

• SoftwareUnderstanding / rolf

  Implementation of a flexible methodology for research software classification

  classificationresearch-softwaremethodologytaxonomic-classification
  Language:Jupyter Notebook 5

• V-Z / sondovac

  Sondovač is a script to create orthologous low-copy nuclear probes from transcriptome and genome skim data for target enrichment. For latest version check "releases".

  sciencephylogeneticsngs-pipelinengs-analysisngsgeneticsmolecular-biologyphylogenomics-pipelinephylogenomicspipelinehybseq-dataorthologuestranscriptomedata-analysisdata-sciencephylogenomictaxonomic-classificationbioinformaticsbioinformatics-pipelinebioinformatics-analysis
  Language:TeX 5

• xapple / crest4

  The `crest4` python package can automatically assign taxonomic names to DNA sequences obtained from environmental sequencing.

  16s-rrnabioinformaticsdna-sequencestaxonomic-classification
  Language:Python 5

• emiliomastriani / PIMGAVir

  PIpeline for MetaGenomic Analysis of Viral reads from 2nd generation sequencer

  2ndbioinformaticsngstaxonomic-classificationviruses
  Language:Shell 4

• faridnec / forecasting-tech-adoption

  Forecasting the Adoption Process of Technology Using ML Methods

  classificationsupervised-learningtimeseries-forecastingpatent-analysispredictive-modelingtaxonomic-classification
  Language:Jupyter Notebook 4

• Rowena-h / FungusNameCheck

  A script to check fungus names for the most up to date nomenclature according to Species Fungorum 🍄

  fungitaxonomic-classification
  Language:R 4

• dalmolingroup / euryale

  A pipeline for taxonomic classification and functional annotation of metagenomic reads. Based on MEDUSA

  diamondfunctional-annotationkaijumetagenomicstaxonomic-classificationnextflowpipelinesnakemake
  Language:Nextflow 3

• AuReMe / esmecata

  From taxonomic affiliations to annotated proteins using UniProt database.

  uniprotproteomestaxonomic-classification
  Language:Python 2

• BCCDC-PHL / 16s-nf

  Prepare a report for taxonomic assignment based on 16S rRNA sequences, using BLAST.

  16s-rrnamicrobial-genomicstaxonomic-classification
  Language:Python 2

• VincentGaoHJ / Taxonomic-Relation-Identification

  Awesome research paper on taxonomy (information retrieval). Study notes about their contributions, methods, and results.

  knowledge-graphembeddingsrelation-extractiontaxonomytaxonomic-classification
  2