Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: taxonomic-classification
metagenopolis/meteor
Meteor is a plateform for quantitative metagenomics profiling of complex ecosystems. Meteor relies on genes catalogue to perform specie level taxonomic assignments and functional analysis.
Language: Python - Size: 67.5 MB - Last synced: 13 days ago - Pushed: 20 days ago - Stars: 6 - Forks: 0
faridnec/forecasting-tech-adoption
Forecasting the Adoption Process of Technology Using ML Methods
Language: Jupyter Notebook - Size: 14.7 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 4 - Forks: 0
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.
Language: JavaScript - Size: 1.44 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 7 - Forks: 0
nf-core/taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Language: Nextflow - Size: 11.9 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 92 - Forks: 30
dalmolingroup/euryale
A pipeline for taxonomic classification and functional annotation of metagenomic reads. Based on MEDUSA
Language: Nextflow - Size: 9 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 3 - Forks: 0
dalmolingroup/MicroView
A reporting tool for aggregating results from taxonomic classification analyses
Language: Python - Size: 1.15 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0
sourcemeta/json-taxonomy
A formal taxonomy to classify JSON documents based on their size, type of content, characteristics of their structure and redundancy criteria.
Language: JavaScript - Size: 1.97 MB - Last synced: 13 days ago - Pushed: 14 days ago - Stars: 6 - Forks: 1
xapple/crest4
The `crest4` python package can automatically assign taxonomic names to DNA sequences obtained from environmental sequencing.
Language: Python - Size: 1.16 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 5 - Forks: 0
bio-org-au/services-g3
Grails 3 port of NSL services
Language: Groovy - Size: 5.99 MB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 0 - Forks: 0
bluenote-1577/sylph
ultrafast genome querying and taxonomic profiling for metagenomic samples by abundance-corrected minhash.
Language: Rust - Size: 27.6 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 102 - Forks: 5
nf-core/ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Language: Nextflow - Size: 14.9 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 157 - Forks: 105
BCCDC-PHL/16s-nf
Prepare a report for taxonomic assignment based on 16S rRNA sequences, using BLAST.
Language: Python - Size: 51.8 KB - Last synced: 21 days ago - Pushed: 22 days ago - Stars: 2 - Forks: 0
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: Python - Size: 967 KB - Last synced: 21 days ago - Pushed: 6 months ago - Stars: 63 - Forks: 7
sourmash-bio/sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
Language: Python - Size: 35 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 431 - Forks: 77
laowantong/paroxython
Tag and recommend Python exercises based on algorithmic features
Language: Python - Size: 7.64 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 33 - Forks: 4
steineggerlab/Metabuli
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
Language: C++ - Size: 16.8 MB - Last synced: 28 days ago - Pushed: 28 days ago - Stars: 62 - Forks: 7
AuReMe/esmecata
From taxonomic affiliations to annotated proteins using UniProt database.
Language: Python - Size: 7.87 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 2 - Forks: 1
mbhall88/classification_benchmark
Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification
Language: Python - Size: 1.15 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 8 - Forks: 0
treangenlab/lemur
Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets
Language: Python - Size: 93.8 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0
bo1929/CONSULT-II Fork of noraracht/CONSULT
Accurate taxonomic classification and abundance profiling using locality-sensitive hashing.
Language: C++ - Size: 21.7 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 2 - Forks: 0
nf-core/detaxizer
A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxa to identify (and remove) are Homo and Homo sapiens. Removal is optional.
Language: Nextflow - Size: 4.16 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 9 - Forks: 3
boalang/quality
Improving data quality of taxonomic assignments in large-scale public databases
Language: Jupyter Notebook - Size: 9.63 MB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 1
hsmurali/Transitive_Annotation
The impact of transitive annotation on the training of taxonomic classifiers
Language: Jupyter Notebook - Size: 2.43 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0
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: Python - Size: 43.9 KB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 44 - Forks: 15
JensUweUlrich/Taxor
Fast and space-efficient taxonomic classification of long reads
Language: C++ - Size: 662 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 14 - Forks: 1
roseedwin/Benchmarking-taxonomic-classifiers-for-soil-shotgun-data
Benchmarking various taxonomic classifiers for profiling soil metagenomic data, with scripts and tools tailored for fungal, bacterial, and archaeal genome identification.
Language: R - Size: 510 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 2 - Forks: 0
bioinformatics-centre/kaiju
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
Language: C - Size: 968 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 241 - Forks: 65
SoftwareUnderstanding/rolf
Implementation of a flexible methodology for research software classification
Language: Jupyter Notebook - Size: 1.13 GB - Last synced: 29 days ago - Pushed: 4 months ago - Stars: 5 - Forks: 1
phylo42/PEWO
Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees
Language: Python - Size: 7.82 MB - Last synced: about 3 hours ago - Pushed: about 17 hours ago - Stars: 11 - Forks: 9
shenwei356/kmcp
Accurate metagenomic profiling && Fast large-scale sequence/genome searching
Language: Go - Size: 82.1 MB - Last synced: 3 months ago - Pushed: 8 months ago - Stars: 167 - Forks: 13
AxZxP/WAG-Results-Forecasting
Autoregression model for predicting results on metrics and Cohort analysis.
Language: Python - Size: 2.13 MB - Last synced: 4 months ago - Pushed: 5 months ago - Stars: 1 - Forks: 0
emiliomastriani/PIMGAVir
PIpeline for MetaGenomic Analysis of Viral reads from 2nd generation sequencer
Language: Shell - Size: 88.8 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 3 - Forks: 2
phylo42/RAPPAS
Rapid, Alignment-free, Phylogenetic Placement via Ancestral Sequences
Language: Java - Size: 47.5 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 9 - Forks: 3
emiliomastriani/Vir-MinION
Pipeline for 3rd Generation sequencing data from MinION
Language: Shell - Size: 48 MB - Last synced: 6 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 1
hermidalc/dragonfish
A fast, efficient, and accurate functional and taxonomic meta-omic profiler built on Pufferfish and the ccdBG
Language: Python - Size: 9.24 MB - Last synced: 6 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0
VincentGaoHJ/Taxonomic-Relation-Identification
Awesome research paper on taxonomy (information retrieval). Study notes about their contributions, methods, and results.
Size: 119 KB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 2 - Forks: 2
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".
Language: TeX - Size: 14.4 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 5 - Forks: 2
millanp95/DeLUCS
This repository contains all the source files required to run DeLUCS, a deep learning clustering algorithm for DNA sequences.
Language: Python - Size: 634 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 22 - Forks: 10
joonahn/assign_taxonomy
Web page for assigning taxonomy of microorganisms.
Language: JavaScript - Size: 27.3 KB - Last synced: 7 months ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0
pierrebarbera/epa-ng
Massively parallel phylogenetic placement of genetic sequences
Language: C++ - Size: 32.5 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 64 - Forks: 7
HKU-BAL/MegaPath
MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data; MegaPath-Amplicon: filtering module for metagenomic amplicon data
Language: Java - Size: 23.2 MB - Last synced: 23 days ago - Pushed: over 2 years ago - Stars: 6 - Forks: 0
microUCPH/amplicon_data_analysis
Collection of notebooks describing the basic analysis workflow for a 16S rRNA gene amplicon sequencing project
Language: HTML - Size: 8.23 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 10 - Forks: 6
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: R - Size: 25.3 MB - Last synced: 9 months ago - Pushed: 11 months ago - Stars: 7 - Forks: 1
kaymers/MetaG_backend
Processing modules of the metagenomic visualization tool, MetaG.
Language: Python - Size: 64.6 MB - Last synced: 10 months ago - Pushed: about 3 years ago - Stars: 1 - Forks: 1
exabiome/gtnet
The Genome Taxonomy Network for assigning microbial taxonomy to DNA sequences
Language: Python - Size: 58.4 MB - Last synced: 10 days ago - Pushed: 2 months ago - Stars: 1 - Forks: 0
Kya-Allen/PyTaxa
A library for performing Taxometric Analysis
Language: Python - Size: 43.1 MB - Last synced: 12 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0
bioinfoUQAM/CASTOR_KRFE
Alignment-free method to identify and analyse discriminant genomic subsequences within pathogen sequences
Language: Python - Size: 2.89 MB - Last synced: 9 months ago - Pushed: about 1 year ago - Stars: 9 - Forks: 2
ali-kishk/AmpliconNet
Sequence based 16S rRNA Taxonomic classifier using MLP
Language: Jupyter Notebook - Size: 296 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 8 - Forks: 0
VSainteuf/metric-guided-prototypes-pytorch
PyTorch implementation of Metric-Guided Prototype Learning for hierarchical classification.
Language: Jupyter Notebook - Size: 3.98 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 20 - Forks: 3
robertfmath/Mammal-Taxonomy-Gradient-Boosting-Classifier
Predicting mammalian taxonomic order based on ecological, geographic, and life-history traits
Language: Jupyter Notebook - Size: 21.5 MB - Last synced: 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
rwst/process-ubiome-16S 📦
process raw reads from ubiome
Language: Python - Size: 10.7 KB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 2 - Forks: 0
peterk87/filter_classified_reads
Filter for reads from taxa of interest using Kraken2/Centrifuge classification results.
Language: Python - Size: 1.53 MB - Last synced: 26 days ago - Pushed: over 1 year ago - Stars: 7 - Forks: 1
maremita/slm_kgenomvir
Evaluation of Statistical Linear Models for Genome Virus Classification
Language: Jupyter Notebook - Size: 3.12 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 1 - Forks: 1
maremita/CASTOR_KRFE_v1.0
[Features extraction method] You can find the new version of CASTOR_KRFE at https://github.com/bioinfoUQAM/CASTOR_KRFE
Language: Python - Size: 1.94 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0
Rowena-h/FungusNameCheck
A script to check fungus names for the most up to date nomenclature according to Species Fungorum
Language: R - Size: 25.4 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0
mariachiaragrieco/TIPre
Taxonomic Identity PREdiction: homework for Machine Learning Course 2021 (MSc Bioinformatics for Computational Genomics)
Language: Jupyter Notebook - Size: 6.29 MB - Last synced: about 1 month ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0
asiort/MiGAscraping
Scrapes all the results of all the genome analysis performed by MiGA Online web tool and wirte them in a file.
Language: Python - Size: 28.3 KB - Last synced: 4 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0
mmtechslv/PhyloMAF
Next Generation Phylogenetic Microbiome Analysis Framework
Language: Python - Size: 86.5 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 1 - Forks: 0
batman32168/gics-icb
This library provides a way to parse, manipulate and analyze ICB and GICS Codes.
Language: Python - Size: 77.1 KB - Last synced: 24 days ago - Pushed: over 2 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: 20 days ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0
omni-species/initiative
The standards proposed by Omni Species for better intercommunicability between the different Biological Systematics platforms.
Size: 1000 Bytes - Last synced: 4 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0
iamarchisha/TCS-HumAIn
Built as a solution to HumAIn, 2019 by TCS.
Language: Jupyter Notebook - Size: 764 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0
ToniWestbrook/mitobin
Taxonomic classification and read binning of mitochondrial DNA
Language: Python - Size: 25.4 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0
ibiom-cnr/MetaShot Fork of bfosso/MetaShot
MetaShot (Metagenomics Shotgun) is a complete pipeline designed for the taxonomic classification of the human microbiota members. In MetaShot, third party tools and new developed Python and Bash scripts are integrated to analyze paired-end (PE) Illumina sequences, offering an automated procedure covering all the analysis steps from raw data management to taxonomic profiling. It is designed to analyze both DNA-Seq and RNA-Seq data.
Language: Python - Size: 1.5 MB - Last synced: about 1 year ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0
smdabdoub/clark-biom
Create BIOM-format tables (http://biom-format.org) from CLARK output (http://clark.cs.ucr.edu/) for use with downstream tools such as UniFrac, iTol (itol.embl.de), or PhyloToAST (phylotoast.org), PhyloToAST (http://phylotoast.org).
Language: Python - Size: 23.4 KB - Last synced: 18 days ago - Pushed: about 6 years ago - Stars: 1 - Forks: 0
kevinxchan/amphibNames
Web application for batch updates of amphibian taxonomies.
Language: JavaScript - Size: 411 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0
rwst/gbff2RDP
create RDP classifier training files from NCBI taxonomy gbff file
Language: Python - Size: 29.3 KB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0
tomarashish/metagenD3
metagenomics visualization library
Language: JavaScript - Size: 751 KB - Last synced: about 1 year ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0
