metagenomic-classification

There are 1 repository under metagenomic-classification topic.

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-taxonomy gtdb ganon kraken2 custom-taxonomy metagenomic-classification custom-database taxonomic-classification taxonomic-classifications centrifuge krakenuniq ncbi-database amplicon 16s
Language:Python 63
muellan / metacache
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
genome read-mapping refseq taxonomy metagenomics metagenomic-analysis metagenomic-classification metagenomes metagenomic-data ncbi-refseq fasta fastq dna-sequences genomic-data-analysis classification bioinformatics bioinformatics-tool bioinformatics-algorithms short-read-mapper long-reads
Language:C++ 55
prophyle / prophyle
Accurate, resource-frugal and deterministic DNA sequence classifier.
metagenomics bwt phylogeny metagenomic-classification bioinformatics bacteria viruses burrows-wheeler-transform k-mers phylogenetic-compression simplitigs prophyle
Language:Python 31
taxpasta
taxprofiler / taxpasta
TAXnomic Profile Aggregation and STAndardisation
metagenomics python standardisation bioinformatics profiling classification metagenomic-classification taxonomic-classifications taxonomic-profiling
Language:Python 31
EBI-Metagenomics / pipeline-v5
This repository contains all CWL descriptions of the MGnify pipeline version 5.0.
common-workflow-language cwl workflow cwl-descriptions cwl-workflow mgnify metagenomic-pipeline metagenomic-analysis metagenomic-classification metagenomic-data metagenomics amplicon-pipeline wgs-analysis
Language:HTML 20
rcs333 / CLOMP
:horse: CLinically Okay Metagenomic Pipeline :horse:
metagenomic-classification metagenomic-data metagenomic-pipeline metagenomics next-generation-sequencing ngs-pipeline sequencing taxonomy
Language:Python 6
hivlab / discover-virome
discover-virome: identify and quantify viruses from metagenomic assemblies
metagenomic-analysis metagenomic-classification snakemake snakemake-workflow virome virome-workflow
Language:Python 3
pfeiferd / genestrip
Genestrip - Efficient read classification, filtering and k-mer counting for selected groups of species
bioinformatics genomes genomic-data-analysis high-performance kmer-counting kraken2 krakenuniq metagenomic-analysis metagenomic-classification pathogen-genomics command-line-tool java
Language:Java 3
sunbeam-labs / sbx_krakenhll
krakenhll metagenomic-classification snakemake sunbeam
3
bo1929 / CONSULT-II
Accurate taxonomic classification and abundance profiling using locality-sensitive hashing.
taxonomic-classification contamination-removal metagenomic-analysis metagenomic-classification metagenomics
Language:C++ 2
laurentnoe / iedera
subset and spaced seed design tool
sequence-alignment indexing spaced-seed read-mapping alignment-free metagenomic-classification sequence-alignments k-mer align
Language:C++ 2
exabiome / gtnet
The Genome Taxonomy Network for assigning microbial taxonomy to DNA sequences
metagenomic-analysis metagenomic-classification metagenomics microbial-taxonomy neural-network taxonomic-classification
Language:Python 1
treangenlab / lemur
Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets
long-read-sequencing long-reads metagenomic-analysis metagenomic-classification metagenomics taxonomic-classification taxonomic-profiling
Language:Python 1
hsmurali / Transitive_Annotation
The impact of transitive annotation on the training of taxonomic classifiers
16s-rrna adversarial-examples blastn taxonomic-classification taxonomy-database error-percolation transitive-annotation amplicon-sequencing metagenomic-classification
Language:Jupyter Notebook 0
Tharos-ux / wisp
XGBoost implementation for bacteria family identification
classification metagenomes metagenomic-analysis metagenomic-classification metagenomics phylogenetics phylogeny
Language:Python 0