Table 3.
Representative tools are organized by their main functionality.
| TOOL | CATEGORY BY MAIN FUNCTION | INPUT DATA TYPE | LICENSE TYPE | IMPLEMENTATION | LAST UPDATE |
|---|---|---|---|---|---|
| FastQC | Quality Control | Raw sequence data (before any alignment or assembly steps) | Open source | Stand-alone | 2023 |
| LongQC[103] | Quality Control | Raw Long-Read Sequencing Data (before any alignment or assembly steps - PacBio Sequencing, Oxford Nanopore Sequencing) | Open source | Stand-alone | 2023 |
| MinIONQC[104] | Quality Control | Raw sequence data (before any alignment or assembly steps - FASTQ, FAST5 format) | Open source | Stand-alone | 2020 |
| NanoPack[105] | Quality Control | Raw sequence data (before any alignment or assembly steps - FASTQ, FAST5 format) | Open source | Suite of tools | 2023 |
| SOAPnuke[106] | Quality Control | Raw sequence data (before any alignment or assembly steps - FASTQ format) | Open source | Stand-alone | 2024 |
| SequelTools[107] | Quality Control | Raw Long-Read Sequencing Data (before any alignment or assembly steps - PacBio Sequencing, Oxford Nanopore Sequencing) | Open source | Stand-alone | 2020 |
| ABySS-Explorer[108] | Assembly | ABySS Assemblies (scaffolds or contigs in FASTA format), Raw sequence data | Open source | Stand-alone | 2018 |
| Assembly Graph Browser (AGB)[109] | Assembly | Assembly Graph Files (GFA (Graphical Fragment Assembly)) | Open source | Stand-alone | 2019 |
| GfaViz[110] | Assembly | Assembly Graph Files (GFA (Graphical Fragment Assembly)) | Open source | Stand-alone | 2019 |
| SGTK[111] | Assembly | Assembly Graph Files (GFA (Graphical Fragment Assembly)) | Open source | Toolkit | Archived in 2023 |
| PanGraphViewer[112] | Assembly/Pangenome | Pangenome graphs (rGFA, GFA_v1, VCF), Annotation Files (BED, GTF / GFF) | Open source | Stand-alone | 2022 |
| MetagenomeScope | Assembly | GFA, FASTG, GML, LastGraph | Open source | Web-based tool | 2020 |
| BinaRena[113] | Binning | (Human) Assembled Data (FASTA) | BSD 3-Clause License | Web application | 2023 |
| CONCOCT[114] | Binning | Metagenomic Sequencing data, Contig Sequence | Open source | Stand-alone | 2019 |
| MetaWRAP[115] | Binning | Metagenomic sequencing data (FASTQ format), Assembled contigs (FASTA), | Open source | Pipeline | 2020 |
| VizBin[116] | Binning | Metagenomic Fragments (Contigs / reads)(FASTA) | BSD License (4-clause) | Stand-alone | 2019 |
| Anvio[117] | Contig & Genome Viewer / Communities / Taxonomy | DNA sequence (FASTA), Contigs (FASTA), Short reads (FASTA), External / Internal genome database | Open source | Stand-alone | 2023 |
| CGViewer.js[118] | Contig & Genome Viewer | JSON files | Open source | Web-based tool | 2019 |
| CRAMER[119] | Contig, Genome & MSA Viewer | Metagenomic sequence data (Raw DNA sequence / FASTA files) | Open source | Stand-alone | 2019 |
| Elviz[120] | Contig & Genome Viewer | Metagenomic sequence data (Raw DNA sequence / FASTA files) | Open source | Web-based application | 2024 |
| GDV[121] | Contig, Genome & MSA Viewer | RNA-seq data, ChIP-seq data, Genome Sequence Data, Proteomic Data & Epigenomic Data | Open source | Web-based application | 2021 |
| Gosling[122] | Contig, Genome & MSA Viewer | Metagenomic sequence data (Raw DNA sequence / FASTA files) | Open source | Toolkit | 2021 |
| IMG/M[23], IMG/VR[30] | Contig and Genome Viewer | Visualization of IMG/M and IMG/VR contig annotations | Open source | Web-based platforms | 2023 |
| IGV[123] | Genome Viewer | Metagenome sequence data (FASTA), Alignment Data, Variant Calls, Gene Annotations (GFF) | Open source | Stand-alone | 2023 |
| JBrowse[124] | Genome Viewer | Metagenome sequence data (FASTA), Alignment Data, Variant Calls, Gene Annotations (GFF) | Open source | Stand-alone | 2024 |
| MetaErg[47] | Contig Viewer | Metagenomic Contig, Gene Prediction File, Taxonomic Information File | Open source | Stand-alone pipeline | 2020 |
| Tablet[125] | Genome Viewer | SAM (Sequence Alignment/Map) and BAM (Binary Alignment/Map), Variant Call Format (VCF), Metagenome Sequence, Genome Assembly Files, Sequence Read Files | BSD-2-Clause license | Stand-alone | 2021 |
| UCSC Genome Browser[126] | Genome & MSA Viewer | Genome Sequence Data, Annotation Data (GFF), ChIP-Seq Data, RNA-seq Data, Multiple Sequence Alignments (MSA) | Open source | Online portal | 2022 |
| ENSEMBL[127] | Genome Viewer | Genome Sequence Data, Annotation Data (GFF), ChIP-Seq Data, RNA-seq Data, Multiple Sequence Alignments (MSA) | Open source | Suite of tools | 2024 |
| Artemis[128] | Genome Viewer | Genome Sequence Data, Annotation Data (Genebank, EMBL format) | Open source | Stand-alone | 2011 |
| UGENE[129] | Genome Viewer | Genome Sequence Data (FASTA, GFF, SAM/BAM, BED), Annotation Data (Genebank, EMBL format, BED, GFF), Multiple Sequence Alignments (MAF), Expression Data Files | Open source | Stand-alone | 2023 |
| Geneious[130] | Genome Viewer | Genome Sequence Data (FASTA, GFF, SAM/BAM, BED), Annotation Data (Genebank, EMBL format, BED, GFF), Multiple Sequence Alignments (MAF), Expression Data Files | Free trial - Requires subscription | Part of a software suite | 2023 |
| BV-BRC[131] | MSA Viewer | Multiple Sequence Alignments (MSA) | Portal | Web-based resource | 2022 |
| MSAViewer[132] | MSA Viewer | Multiple Sequence Alignments (MSA) | Open source | Web-based application | 2023 |
| Strudel[133] | MSA Viewer | Metadata (CSV,TSV), Aligned Sequence Data, Phylogenetic Tree Data, Annotation Data (GFF) | Open source | Stand alone | 2015 |
| SuiteMSA[134] | MSA Viewer | Multiple Sequence Alignments (MSA) | Open source | Stand alone | 2013 |
| JalView[135] | MSA Viewer | Multiple Sequence Alignments (ex FASTA, Clustal, Stockholm) | Open source | Stand alone | 2023 |
| MSABrowser[136] | MSA Viewer | Multiple Sequence Alignments (MSA) | Open source | Stand-alone web-based application | 2021 |
| Seaview[137] | MSA Viewer | Multiple Sequence Alignments (ex FASTA, Clustal, Stockholm, PHYLIP) | Open source | Stand-alone or helper application | 2024 |
| Panache[138] | Pangenome Viewer | Graphical Fragment Assembly (GFA) | Open source | Web-based interface | 2022 |
| Pan-Tetris[139] | Pangenome Viewer | Pangenome map files (ex PanGee), meta-information (TIGRFAM) | Open source | Software tool | 2015 |
| PanViz[140] | Pangenome Viewer | Pangenome Matrix (pattern of each gene group) and functional annotation files (GeneOntology) | Open source | Pipeline | 2017 |
| PanX[141] | Pangenome Viewer | Set of annotated bacterial strains (NCBI RefSeq, users input in GeneBank format) | Open source | Pipeline | 2018 |
| Pantools[142] | Pangenome & Panproteome Viewer | Annotation Files (GTF / GFF), Multiple Sequence Alignment File (FASTA), Genomic Sequence Files (FASTA), Variations adding (VCF files and a PAV table) | Open source | Stand-alone | 2024 |
| Bifrost[143] | Pangenome Viewer | Annotation Files (GTF / GFF), Multiple Sequence Alignment File (FASTA), Genomic Sequence Files (FASTA), | Open source | Stand-alone | 2024 |
| PanGenome Graph Builder[144] | Pangenome Viewer | Annotation Files (GTF / GFF), Multiple Sequence Alignment File (FASTA), Genomic Sequence Files (FASTA) | Open source | Stand-alone | 2024 |
| TwoPaCo[145] | Pangenome Viewer | Annotation Files (GTF / GFF), Multiple Sequence Alignment File (FASTA), Genomic Sequence Files (FASTA) | Open source | Stand-alone | 2022 |
| Minigraph-Cactus[146] | Pangenome Viewer | Annotation Files (GTF / GFF), Multiple Sequence Alignment File (FASTA), Genomic Sequence Files (FASTA) | Open source | Pipeline | 2024 |
| Jasper/Microbiome Maps[147] | Abundance analysis / Taxonomy / Ecosystem visualization | Abundance profiles / OTU table | Not open source | Stand-alone | 2023 |
| QIIME / QIIME 2[148] | Communities/ Taxonomy | raw DNA sequence reads | Open source | Analysis package | 2024 |
| Phyloseq[149] | Communities/ Taxonomy | OTU table (operational taxonomic units), phylogenetic tree | Open source | R package | 2013 |
| MicrobiomeAnalyet[150] | Communities/ Taxonomy/PCA visualization | OTU table (operational taxonomic units), taxon list, gene list, Gene abundance table, BIOM file | Open source | Web-based platform | 2024 |
| MetagenomeSeq[151] | Communities/ Taxonomy/PCA visualization | Taxonomic or Functional Annotations, Count Data Table | Open source | R package | 2019 |
| MEGA[152] | Taxonomy | Metagenome sequence data (FASTA), Phylogenetic Data (NEXUS, NEWICK) | Open source | Can be used as stand-alone and as part of a pipeline | 2022 |
| PAUP[153] | Taxonomy | Metagenome sequence data (FASTA), Phylogenetic Data (NEXUS, NEWICK) | Proprietary, and thus commercial | Stand-alone | 2007 |
| FigTree | Taxonomy | Phylogenetic Data (NEXUS, NEWICK) | Open source | Stand-alone | 2018 |
| iTOL[154], [155] | Taxonomy | Phylogenetic Data (NEXUS, NEWICK) | Open source | Web-based platform | 2023 |
| PhyD3[156] | Taxonomy | Phylogenetic Data (NEXUS, NEWICK) | Open source | Web-based tool | 2017 |
| Dendroscope[157] | Taxonomy (viewer) | Phylogenetic Data (NEXUS, NEWICK) | Open source | Stand-alone | 2023 |
| Cytoscape[158], [159] | Network visualization | Graphs - Lists (source - destination) | Open source | Stand-alone | 2023 |
| Gephi[160] | Network visualization | Graphs - Lists (source - destination) | Open source | Stand-alone | 2023 |
| Pajek[161] | Network visualization Large Networks |
Has its file format | Open source | Stand-alone | 2023 |
| Arena3Dweb[162], [163] | Network visualization 3D Multilayered Networks |
Network lists (source - destination but by defining their layers) | Open source | Web server and stand-alone | 2023 |
| NORMA[164], [165] | Network and group visualization | Network lists (source - destination) and annotation files (nodes and the annotation group they belong to) | Open source | Web server and stand-alone | 2022 |