Quickly search, compare, and analyze genomic and metagenomic data sets.
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Updated
Sep 9, 2024 - 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 )
Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes
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
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.
process raw reads from ubiome
From taxonomic affiliations to annotated proteins using UniProt database.
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).
The Genome Taxonomy Network for assigning microbial taxonomy to DNA sequences
This library provides a way to parse, manipulate and analyze ICB and GICS Codes.
Autoregression model for predicting results on metrics and Cohort analysis.
Processing modules of the metagenomic visualization tool, MetaG.
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