Amplicon sequencing analysis workflow using DADA2 and QIIME2
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Updated
Aug 6, 2024 - Nextflow
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Quickly search, compare, and analyze genomic and metagenomic data sets.
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
Accurate metagenomic profiling && Fast large-scale sequence/genome searching
This repository contains all the source files required to run DeLUCS, a deep learning clustering algorithm for DNA sequences.
Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )
Massively parallel phylogenetic placement of genetic sequences
Collection of notebooks describing the basic analysis workflow for a 16S rRNA gene amplicon sequencing project
ultrafast genome querying and taxonomic profiling for metagenomic samples by abundance-corrected minhash.
Tag and recommend Python exercises based on algorithmic features
PyTorch implementation of Metric-Guided Prototype Learning for hierarchical classification.
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.
Implementation of a flexible methodology for research software classification
Rapid, Alignment-free, Phylogenetic Placement via Ancestral Sequences
Alignment-free method to identify and analyse discriminant genomic subsequences within pathogen sequences
PIpeline for MetaGenomic Analysis of Viral reads from 2nd generation sequencer
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