CoReMicrob: Computational Resources for Micorbiome

Major Taxonomy Assignment tools for Whole Metagenome in Microbiome data

Tools used for Taxonomy Assignment of Whole Metagenome Data

Tool Name Description PubMed ID
phyloFlash Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenome 33109753
Kraken2 Ultrafast and accurate 16S rRNA microbial community analysis tool 32859275
16S Classifier A Tool for Fast and Accurate Taxonomic Classification of 16S rRNA Hypervariable Regions in Metagenomic Datasets 25646627
EzBioCloud a genome-driven database and platform for microbiome identification and discovery 38888585
SPINGO a rapid species-classifier for microbial amplicon sequences 26450747
Sintax A simple non-Bayesian taxonomy classifier for 16S and ITS sequences bioRxiv
Vsearch The tools for OTU clustering, diversity analyses, and taxonomic assignment. 27781170
MOCHI These analyses make use of 16S/18S rRNA gene sequencing to identify taxa and predict species diversity. 35876544
PM-profiler a high-resolution and fast tool for taxonomy annotation of amplicon-based microbiome 38912828
LotuS2 an ultrafast and highly accurate tool for amplicon sequencing analysis 36258257
RDP Classifier An machine learning approaches for taxonomic classification for 16s and 26s sequencing 38436268
FungiLT A Deep Learning Approach for Species-Level Taxonomic Classification of Fungal ITS Sequences MDPI
Hitac A hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2 38956506
Kaiju Fast and sensitive taxonomic classification for metagenomics 27071849
Kraken Ultrafast metagenomic sequence classification using exact alignments 24580807
Bracken Estimating species abundance from Kraken output PeerJ
CLARK Fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers 25879410
k-SLAM Accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets 27965413
MetaPhlAn4 Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4 36823356
PanPhlAn3 A strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples. 33944776
IGGsearch Marker based taxonomy assignment 30867587
KrakenUniq Confident and fast metagenomics classification using unique k-mer counts 30445993
Centrifuge Rapid and sensitive classification of metagenomic sequences 27852649
MetaCache Context-aware classification of metagenomic reads using minhashing 28961782
VirusTaxo Taxonomic classification of viruses from the genome sequence using k-mer enrichment 35718090
Taxonomer An interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling 27224977
LMAT Taxonomic classification, content summarization and gene identification: all-in-1 metagenomic analysis toolkit 23828782
Sourmash A k-mer analysis multitool providing stable, robust programmatic and command-line APIs for a variety of sequence comparisons 31508216
metaOthello A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures 29036588
ProPhyle Accurate and resource-frugal phylogeny-based metagenomic classification bioRxiv
TaxMaps An ultra-efficient, customizable and fully scalable taxonomic classification tool for short-read data 29588360
MetaBIDx A new computational approach to bacteria identification in microbiomes 38841411
StrainGE A toolkit to track and characterize low-abundance strains in complex microbial communities 35255937
SameStr Identification of a persisting core gut microbiota transferable by fecal transplantation 35337386
taxMaps Comprehensive and highly accurate taxonomic classification of short-read data in reasonable time 29588360
CLARK-S A new software tool that can classify short reads with high precision, high sensitivity and high speed. 27540266
ViromeScan A BLAST based tool for metagenomic viral community profiling 26932765
VISTA A Tool for Fast Taxonomic Assignment of Viral Genome Sequences 39540753
VITAP A high precision tool for DNA and RNA viral classification based on meta-omic data 40044690
ViTax Adaptive hierarchical viral taxonomy classification with a taxonomy belief tree on a foundation model 39921398
VirTAXA Enhancing RNA virus taxonomic classification with remote homology search and tree-based validation 39325874
VIRify An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models 37639475
MiCoP A microbial community profiling method for detecting viral and fungal organisms in metagenomic samples 31167634
HumanMycobiomeScan A BLAST based tool for the characterization of the fungal fraction in metagenomic samples 31202277
FunOMIC Pipeline with built-in fungal taxonomic and functional databases for human mycobiome profiling 35891785
EukDetect Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing 33658077

Tools used for Strain-Profiling from Whole Metagenome Data

Tool Name Description PubMed ID
ConStrain Identifies microbial strains in metagenomic datasets 26344404
StrainFinder Strain Finder takes as input a reference genome alignment and the number of strains to infer 29447696
StrainEst Strain profiling and epidemiology of bacterial species from metagenomic sequencing 29273717
StrainPhlAn3 A metagenomic strain-level population genomics tool 33944776
MMseqs2 Fast and sensitive taxonomic assignment to metagenomic contigs 33734313
GOTTCHA Accurate read-based metagenome characterization using a hierarchical suite of unique signatures 25765641
DeepVirFinder Identifying viruses from metagenomic data using deep learning 34084563
DUDes A top-down taxonomic profiler for metagenomics 27153591
MCP Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets 33959106
MIDAS Metagenomic Intra-species Diversity Analysis System 36321886
PathoScope A complete computational framework for strain identification in environmental or clinical sequencing samples 25225611
StrainSifter Precision identification of diverse bloodstream pathogens in the gut microbiome 30323331
Sigma Strain-level inference of genomes from metagenomic analysis for biosurveillance 25266224
SPARSE Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes RCMB
metaMLST Multi-locus strain-level bacterial typing from metagenomic samples 27651451
PanPhlAn Strain-level microbial epidemiology and population genomics from shotgun metagenomics 26999001
metaSNV Detection of SNVs and subspecies in prokaryotic metagenomes 34791031
DESMAN DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. 28934976
mOTUs2 Microbial abundance, activity and population genomic profiling with mOTUs2 30833550
SNVPhyl A single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology 29026651
PathoScope 2.0 Strain-level inference of genomes from metagenomic analysis for biosurveillance 25266224
VirStrain A strain identification tool for RNA viruses 35101081

Tools used for Growth Rate Analysis

Database Name Description PubMed ID
GRiD High throughput in situ metagenomic measurement of bacterial replication at ultra-low sequencing coverage 30470746
iRep Method for determining replication rates for bacteria from single time point metagenomics sequencing and draft-quality genomes. 27819664
DEMIC Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples 30420687
growthpred The systemic imprint of growth and its uses in ecological (meta)genomics 20090831