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Search results for metagenomics
metagenomics
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276 search results found
Mmseqs2
⭐
1,235
MMseqs2: ultra fast and sensitive search and clustering suite
Vsearch
⭐
605
Versatile open-source tool for microbiome analysis
Megahit
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442
Ultra-fast and memory-efficient (meta-)genome assembler
Gtdbtk
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440
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Dada2
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428
Accurate sample inference from amplicon data with single nucleotide resolution
Anvio
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396
An analysis and visualization platform for 'omics data
Atlas
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332
ATLAS - Three commands to start analyzing your metagenome data
Pavian
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328
🌈 Interactive analysis of metagenomics data
Squeezemeta
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308
A complete pipeline for metagenomic analysis
Training Material
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284
A collection of Galaxy-related training material
Metaphlan
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242
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
Kaiju
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236
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
Dram
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214
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
Krakenuniq
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201
🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
Drep
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199
Rapid comparison and dereplication of genomes
Biomartr
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198
Genomic Data Retrieval with R
Mag
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164
Assembly and binning of metagenomes
Kmcp
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161
Accurate metagenomic profiling && Fast large-scale sequence/genome searching
Insilicoseq
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158
🚀 A sequencing simulator
Sunbeam
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157
A robust, extensible metagenomics pipeline
Metagem
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155
💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
Microbiomemarker
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151
R package for microbiome biomarker discovery
Dashing
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147
Fast and accurate genomic distances using HyperLogLog
Metaeuk
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142
MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
Ampliseq
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141
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Ngless
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141
NGLess: NGS with less work
Computationalgenomicsmanual
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135
Robs manual for the computational genomics and bioinformatics class.
Pb Metagenomics Tools
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127
Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics
Dnanalyzer
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122
Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools
Decontam
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122
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
Metacoder
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121
Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
Camisim
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115
CAMISIM: Simulating metagenomes and microbial communities
Spacegraphcats
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112
Indexing & querying large assembly graphs -- in space, no one can hear you miao!
Eager
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112
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Rapdtool
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110
Rapid Profiling and Deconvolution Tool for Metagenomes
Skani
⭐
101
Fast, robust ANI and aligned fraction for metagenomic genomes and contigs.
Viralrecon
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101
Assembly and intrahost/low-frequency variant calling for viral samples
Plass
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99
Protein-Level ASSembler (PLASS): sensitive and precise protein assembler
Tools Microbiome Analysis
⭐
95
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
Semibin
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89
SemiBin: metagenomics binning with self-supervised deep learning
Maaslin2
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86
MaAsLin2: Microbiome Multivariate Association with Linear Models
Recentrifuge
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83
Recentrifuge: robust comparative analysis and contamination removal for metagenomics
Metagraph
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81
Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly
Graphbin
⭐
80
✨🧬 Refined binning of metagenomic contigs using assembly graphs
Taxprofiler
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78
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Czid Web
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75
Infectious Disease Sequencing Platform
Sylph
⭐
74
ultrafast genome querying and taxonomic profiling for metagenomic shotgun samples by abundance-corrected minhash.
Ganon
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73
ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
Lambda
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70
LAMBDA – the Local Aligner for Massive Biological DatA
Bonsai
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68
Bonsai: Fast, flexible taxonomic analysis and classification
Metagenomics Index Correction
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67
Catch
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63
A package for designing compact and comprehensive capture probe sets.
Aviary
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62
A hybrid assembly and MAG recovery pipeline (and more!)
Ancientmetagenomedir
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61
Repository containing lists of all published ancient metagenomic (and related) samples and libraries
Deepmicrobes
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61
DeepMicrobes: taxonomic classification for metagenomics with deep learning
Ggpicrust2
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59
Make Picrust2 Output Analysis and Visualization Easier
Woltka
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58
Woltka: a versatile meta'omic data classifier
Phables
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56
🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
Fastv
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56
An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.
Metabuli
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54
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
Flashweave.jl
⭐
52
Inference of microbial interaction networks from large-scale heterogeneous abundance data
Funcscan
⭐
49
(Meta-)genome screening for functional and natural product gene sequences
Metacache
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49
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
Macrel
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48
Predict AMPs in (meta)genomes and peptides
Metapi
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46
A general metagenomics data mining system focus on robust microbiome research
Gecco
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45
GEne Cluster prediction with COnditional random fields.
Microbiomebestpracticereview
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45
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
Grabseqs
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44
A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA
Metagenomics_summer_school
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43
Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in December
Groot
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43
A resistome profiler for Graphing Resistance Out Of meTagenomes
Fastq Screen
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42
Detecting contamination in NGS data and multi-species analysis
Metachip
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42
Horizontal gene transfer (HGT) identification pipeline
Struo2
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42
Scalable creating/updating of metagenome profiling databases
Mg Rast
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42
The MG-RAST Backend -- the API server
Keggcharter
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40
A tool for representing genomic potential and transcriptomic expression into KEGG pathways
Struo
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40
Ley Lab MetaGenome Profiler DataBase generator
Bhattlab_workflows
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39
Computational workflows for metagenomics tasks, by the Bhatt lab
Panphlan
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39
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
Metacoag
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36
🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs
Autometa
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35
Autometa: Automated Extraction of Genomes from Shotgun Metagenomes
Datest
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34
Compare different differential abundance and expression methods
Traitar
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34
From genomes to phenotypes: Traitar, the microbial trait analyzer
Strainy
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33
Graph-based assembly phasing
Kraken Biom
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33
Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
Covid 19 Signal
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32
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
Simka
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31
Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.
Mosca
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31
Meta-Omics Software for Community Analysis
Charcoal
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31
Remove contaminated contigs from genomes using k-mers and taxonomies.
Prophyle
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30
Accurate, resource-frugal and deterministic DNA sequence classifier.
Wochenende
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30
Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3
Strainscan
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30
High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers
Fegenie
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29
HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes
Microbiomeutilities
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29
The is mostly a wrapper tool using phyloseq and microbiome R packages.
Nonpareil
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29
Estimate metagenomic coverage and sequence diversity
Metarep
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28
METAREP: JCVI Metagenomics Reports - an open source tool for high-performance comparative metagenomics
Metagenomecourse2019
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28
Course material for the metagenomics course
Zol
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28
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
Bio Py
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27
Some useful python scripts for biologists
Mmlong2
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26
An all-in-one genome-centric metagenomics workflow using long reads
Virnet
⭐
26
VirNet: A deep attention model for viral reads identification
Related Searches
Python Metagenomics (148)
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