Quickly search, compare, and analyze genomic and metagenomic data sets.
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Updated
Jan 21, 2025 - Python
Quickly search, compare, and analyze genomic and metagenomic data sets.
FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )
Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes
Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
Tag and recommend Python exercises based on algorithmic features
This repository contains all the source files required to run DeLUCS, a deep learning clustering algorithm for DNA sequences.
Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets
Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees
Taxonomy classification of viral sequences / contigs
Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification
Alignment-free method to identify and analyse discriminant genomic subsequences within pathogen sequences
Filter for reads from taxa of interest using Kraken2/Centrifuge classification results.
The `crest4` python package can automatically assign taxonomic names to DNA sequences obtained from environmental sequencing.
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
VirusTaxo: Taxonomic classification of viruses from sequence
process raw reads from ubiome
Prepare a report for taxonomic assignment based on 16S rRNA sequences, using BLAST.
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).
This library provides a way to parse, manipulate and analyze ICB and GICS Codes.
The Genome Taxonomy Network for assigning microbial taxonomy to DNA sequences
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