taxonomic-classification

There are 79 repositories under taxonomic-classification topic.

  • sourmash

    sourmash-bio/sourmash

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

    Language:Python522161.9k87

  • bioinformatics-centre/kaiju

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

    Language:C2781427667

  • bluenote-1577/sylph

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

    Language:Rust2214389

  • nf-core/ampliseq

    Amplicon sequencing analysis workflow using DADA2 and QIIME2

    Language:Nextflow217170377143
  • kmcp

    shenwei356/kmcp

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

    Language:Go19754913

  • nf-core/taxprofiler

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

    Language:Nextflow16117421657

  • steineggerlab/Metabuli

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

    Language:C++13264311

  • refresh-bio/vclust

    Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes

    Language:Python893184

  • pierrebarbera/epa-ng

    Massively parallel phylogenetic placement of genetic sequences

    Language:C++8412537

  • 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 )

    Language:Python652378

  • 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).

    Language:Python5522317

  • JensUweUlrich/Taxor

    Fast and space-efficient taxonomic classification of long reads

    Language:C++432142

  • laowantong/paroxython

    Tag and recommend Python exercises based on algorithmic features

    Language:Python344124

  • VSainteuf/metric-guided-prototypes-pytorch

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

    Language:Jupyter Notebook27334

  • millanp95/DeLUCS

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

    Language:Python251711

  • treangenlab/lemur

    Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets

    Language:Python23341

  • nf-core/detaxizer

    A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.

    Language:Nextflow21184105

  • flefler/CyanoSeq

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

    16240

  • dalmolingroup/euryale

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

    Language:Nextflow14130

  • mbhall88/classification_benchmark

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

    Language:Python1220

  • phylo42/PEWO

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

    Language:Python123169

  • rcedgar/viratax

    Taxonomy classification of viral sequences / contigs

    Language:Python12101

  • 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

    Language:R122131

  • microUCPH/amplicon_data_analysis

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

    Language:HTML11186

  • bioinfoUQAM/CASTOR_KRFE

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

    Language:Python10403

  • phylo42/RAPPAS

    Rapid, Alignment-free, Phylogenetic Placement via Ancestral Sequences

    Language:Java93123

  • ali-kishk/AmpliconNet

    Sequence based 16S rRNA Taxonomic classifier using MLP

    Language:Jupyter Notebook8400

  • CMU-SAFARI/MegIS

    MegIS is the first in-storage processing system designed to significantly reduce the data movement overhead of the end-to-end metagenomic analysis pipeline. Described in the ISCA 2024 paper by Mansouri Ghiasi et al.: https://arxiv.org/pdf/2406.19113

    Language:Python740

  • earizon/txt_world_domination

    Markdown extensions to create powerful "Databaseless" CMS: Content is just (git friendly) markdown with multidimensional topic/tags/taxonomy extensions that both humans and AI will appreciate. No need for database servers and binary formats. Human and IA LLM readable plain text is all you need to to conquer the World.

    Language:JavaScript7200

  • peterk87/filter_classified_reads

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

    Language:Python7321

  • HKU-BAL/MegaPath

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

    Language:Java6730

  • omics-lab/VirusTaxo

    VirusTaxo: Taxonomic classification of viruses from sequence

    Language:Python6121

  • SoftwareUnderstanding/rolf

    Implementation of a flexible methodology for research software classification

    Language:Jupyter Notebook62141

  • sourcemeta-research/json-taxonomy

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

    Language:JavaScript6121

  • emiliomastriani/PIMGAVir

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

    Language:Shell5104

  • steineggerlab/taxoview

    A Vue.js plugin for generating interactive Sankey diagrams using Kraken report data

    Language:Vue51