TABLE 2.
Bioinformatic tools used in the multi-omics analysis.
| Name | Application | Databases | Citation |
| Megan | A multitool for taxonomic and functional analysis of metagenomes and amplicon profiles with a graphical user interface and options for PCoA and cluster analysis. | NCBI nr protein for eggNOG, InterPro2GO and SEED, NCBI nucleotide database, Silva SSU and LSU rRNA databases, KEGG (for Ultimate edition only). | Huson et al., 2007, 2016 |
| Qiime 2 | Integrating multiple algorithms for analyzing amplicon sequencing data from quality control to taxonomic identification. Also suitable for analyzing diversity and richness. | Silva SSU and LSU rRNA databases, Greengenes 16S rRNA database, Unite ITS database, custom made databases are also supported. | Hall and Beiko, 2018; Bolyen et al., 2019 |
| Dada2 | An open-source R package for modeling and correcting Illumina amplicon sequencing errors. It is also suitable for taxonomy assignment. Output data can be imported into Phyloseq for further analysis. It is also implemented in Qiime2. | RDP, Greengenes, Silva SSU and LSU rRNA databases, Unite (for fungal taxonomy), custom made databases are also supported. | Callahan et al., 2016 |
| Phyloseq | An open-source R package for a variety of analysis like diversity multi-table comparison etc. | none | McMurdie and Holmes, 2013 |
| Vsearch | A versatile open-source tool for the evaluation of amplicon sequencing also implemented into Qiime2. | Uchim “Gold” database (for chimera filtering if not de novo chimera search is used), Greengenes, Silva SSU and LSU rRNA databases, Unite (for fungal taxonomy), custom made databases are also supported. | Rognes et al., 2016 |
| Diamond | A fast sequence aligner for protein and translated DNA sequences working up to 20000 times faster than BLAST. Can be used as stand-alone but the output is compatible with other softwares, such as Megan. | NCBI nr or other protein databases. Custom made databases are also supported. | Buchfink et al., 2014 |
| Kaiju | A fast k-mer based sequence taxonomy assignment for reads of whole metagenomics or metatranscriptomics data. | There is a number of protein databases prebuilt from the NCBI, Mar and RVB-prot. Costume databases are also supported. | Menzel et al., 2016 |
| Kraken 2 | K-mer based taxonomic sequence classifier. | A number of protein and nucleotide databases are available like RefSeq, NCBI nr and nt, UniVec_Core etc… | Wood et al., 2019 |
| SPAdes/metaSPAdes | MetaSPAdes is designed for assembling shotgun metagenomic reads. It is relying on Spades. | none | Nurk et al., 2017 |
| Idba-UD | Open source de Bruijn graph assembler for single-cell and metagenomic sequencing data. | none | Peng et al., 2012 |
| MEGAHIT | Open source ultra-fast assembler optimized for metagenomics data. | none | Li et al., 2015 |
| Metabat 2 | Adaptive binning algorithm using tetranucleotide frequency and abundance scores for recovering MAGs from Metagenomic data. | none | Kang et al., 2015, 2019 |
| MaxBin 2 | Binning software for recovering MAGs. | none | Wu et al., 2015 |
| Concoct | Binning software for recovering MAGs. | none | Alneberg et al., 2014 |
| Metawrap | A pack of tools for assembling metagenomes, binning, refining and annotating MAGs. | NCBI nr database | Uritskiy et al., 2018 |
| DAS Tool | A bin refinement software. | none | Sieber et al., 2018 |
| checkM | A pack of tools for assessing the quality of genomes and MAGs. | Own database with high-quality genomes to establish the marker genes for bin identification. | Parks et al., 2015 |
| MAGpy | A pipeline for downstream analysis of MAGs. | Uniprot, Sourmash, Pfam, checkM. | Stewart et al., 2018 |
| PhylophlAn | A pipeline for large-scale phylogenetic profiling of genomes and metagenomes. | Marker gene databases: PhyloPhlAn, AMPHORA2. | Asnicar et al., 2020 |
| Galaxy | A web-based tool collection for multiple omics analysis. | Multiple databases. | Afgan et al., 2018 |
| MG-RAST | Web-based service for microbiome studies. | Multiple databases. | Keegan et al., 2016 |
| MGnify | A web-based pipeline by EBI for microbiome studies. | Multiple databases. | Mitchell et al., 2020 |
| OneCodex | A fast web-based pipeline for microbiome studies contains free and paid services. | RefSeq and OneCodex databases. | Minot et al., 2015 |