Table 2.
Lists of software's used in metagenomics analysis.
| Software | Application | Link (website) | References |
|---|---|---|---|
| FastQC | FastQC, a java based application is performed via a series of analysis modules. FastQC can either run in a non-interactive mode or in a standalone interactive mode. FastQC is a quality control tool used for high-throughput sequence data via a series of modular options and giving graphical results of length distribution, quality per base sequence, N numbers, GC content, over representation and duplication. |
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | (175) |
| Fastx-Toolkit | Fastx is a command based tool kit for the quality control of short-reads and allows processing, format conversion, collapsing and cutting on the basis of sequence identity and length. | http://hannonlab.cshl.edu/fastx_toolkit/index.html | (176) |
| PRINSEQ | A standalone tool allows integration and analysis into the existing data processing pipelines. PRINSEQ as a tool offers a computational resource that is able to handle huge amount of data generated by next-generation sequencers. It is used for sequences trimming based on in the di-nucleotides occurrences and the sequence duplication (mainly 5′/3′). | http://prinseq.sourceforge.net/ | (177) |
| NGS QC Toolkit | NGS QC Toolkit encompasses user-friendly standalone tools for the quality control of the sequence data generated by next-generation sequencing platforms. The analysis is performed in a parallel environment. | http://www.nipgr.res.in/ngsqctoolkit.html | (178) |
| Meta-QC-Chain | Meta-QC-Chain is a tool for the quality control analysis performed in parallel environment. Performs mapping against 18S rRNA databases in order to remove the eukaryotic contaminant sequences. | http://www.computationalbioenergy.org/qc- chain.html | (179) |
| Mothur | Mothur is an open-source, expandable software used for the quality analysis of reads to taxonomic classification, ribosomal gene meta-profiling comparison and calculus of diversity estimators. | http://www.mothur.org/ | (180) |
| QIIME | QIIME pipeline is designed for the task of analyzing microbial communities sampled via a marker gene (16S or 18S rRNA) amplicon sequencing. In its heart pipeline QIIME performs quality pre-treatment of raw-reads, calculate estimates diversity estimates, taxonomic annotation and comparison of metagenomic data. | http://qiime.org/ | (181) |
| MEGAN | MEGAN is a graphical interface tool that allows both taxonomic as well as functional analysis of metagenomic reads. It is based on the BLAST output of short reads and performs comparative metagenomics. | http://ab.inf.uni-tuebingen.de/software/megan/ | (20) |
| CARMA | CARMA provides a clear quantitative and statistical characterization of phylogenetic classification of the reads based on Pfam conserved domains. | http://omictools.com/carma-s1021.html | (182) |
| PICRUSt | PICRUSt is a tool that serves in the field of metagenomic analysis where the prediction of the metabolic potential is done from the taxonomic information obtained via 16S rRNA meta-profiling projects. PICRUSt could be thought of as an automated substitute to manually mining the gene families that are believed to be present in organisms whose sequences are found in a 16S ribosomal RNA. | http://picrust.github.io/picrust/ | (183) |
| TETRA | TERTA is a web-based stand alone program used for the Taxonomic classification and comparison of tetra nucleotide patterns with in a DNA sequence. | http://www.megx.net/tetra | (184) |
| PhylophytiaS | Composition-based classifier of sequences based on reference genomes signatures | https://omictools.com/pps-tool | (185) |
| MOCAT | MOCAT is a highly configurable and modular pipeline that includes the quality treatment of metagenomic reads based on single copy marker genes classification and gene-coding prediction. The pipeline makes use of a state-of-the-art program to map quality control and assemble reads from metagenome samples sequenced at a very high depth (several billion base pairs). | http://www.bork.embl.de/mocat/ | (186) |
| Parallel-meta | Parallel-meta is a comprehensive and automotive software package that offers fast data mining and metabolic function across large number of metagenomic datasets. The functional annotation is based on BLAST best hit results. | http://www.computationalbioenergy.org/parallel-meta.html | (187) |
| MetaclusterTA | MetaclusterTA is a tool used for the Taxonomic annotation that is based on the binning of reads and contigs. Dependent on reference genomes. | http://i.cs.hku.hk/~alse/MetaCluster/ | (188) |
| MaxBin | MaxBin software is used for the unsupervised binning of metagenomic sequences based on an Expectation-maximization algorithm. For user's expediency MaxBin reports genome-related statistics including GC content, genome size and completeness. | http://bowtie-bio.sourceforge.net/index.shtml | (189) |
| Amphora and Amphora2 | Amphora and Amphora2 is used for the Metagenomic phylotyping via single copy phylogenetic marker genes classification. | http://pitgroup.org/amphoranet/ | (102, 190) |
| BWA | BWA is an algorithm used for the mapping of short-low-divergent sequences to large references. It is based on Burrows–Wheeler transform. | http://bio-bwa.sourceforge.net/ | (191) |
| Bowtie | Bowtie is a fast short read aligner to long reference sequences based on Burrows–Wheeler transform. | http://bowtiebio.sourceforge.net/index.shtml | (192) |
| Genometa | Genometa is a graphical interface applied for taxonomic and functional annotation of short-reads metagenomic data. | http://genomics1.mhhannover.de/genometa/ | (193) |
| SOrt-ITEMS | SOrt-Items is a tool used for taxonomic annotation via alignment-based orthology of metagenomic reads. | https://omictools.com/sort-items-tool | (194) |
| DiScRIBinATE | Taxonomic assignment by BLASTx best hits classification of reads. | https://www.westgrid.ca/support/software/discribinate | (195) |
| IDBA-UD | IDBA-UD is a denovo assembler of metagenomic sequences with uneven depth. | http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/ | (196) |
| MetaVelvet | MetaVelvet is a denovo assembler of metagenomic short reads. | http://metavelvet.dna.bio.keio.ac.jp/ | (197) |
| RayMeta | RayMeta, a denovo assembler of metagenomic reads and taxonomy profiler by Ray Communities. | http://denovoassembler.sourceforge.net/ | (198) |
| MetaGeneMark | MetaGeneMark is a gene coding sequences predictor from metagenomic sequences by heuristic model. | http://exon.gatech.edu/index.html | (199) |
| GlimmerMG | GlimmerMG is a gene coding sequences predictor from metagenomic sequences by unsupervised clustering. | http://www.cbcb.umd.edu/software/glimmer-mg/ | (200) |
| FragGeneScan | FragGeneScan is a gene coding sequences predictor from short reads. | http://sourceforge.net/projects/fraggenescan/ | (201) |
| CD-HIT | CD-HIT is a tool used for clustering and comparing of sequences of nucleotides or protein. | http://weizhongli-lab.org/cd-hit/ | (202) |
| HMMER3 | HMMER3 is a free and commonly used software package for sequence analysis. It is a Hidden Markov based model used to perform sequences alignments. Used for the identification of the homologus nucleotide and protein sequences | http://hmmer.janelia.org/ | (203) |
| BLASTX | Basic local alignment of translated sequences | http://blast.ncbi.nlm.nih.gov/blast/Blast.cgi | (203) |
| MetaORFA | MetaORFA is applied for the assembly of peptides obtained from predicted ORFs. | Website not available | (204) |
| MinPath | MinPath is a tool used for reconstruction of pathways from protein family predictions. | http://omics.informatics.indiana.edu/MinPath/ | (205) |
| MetaPath | MetaPath is used for the identification of metabolic pathways that are differentially abundant within the metagenomic samples. | http://metapath.cbcb.umd.edu/ | (206) |
| GhostKOALA | GhostKOALA is KEGG's internal annotator of metagenomes by k-number assignment by GHOSTX searches against a non-redundant database of KEGG genes. | http://www.kegg.jp/ghostkoala/ | (207) |
| RAMMCAP | RAMMCAP is used for the metagenomic functional annotation and data clustering. | http://weizhong-lab.ucsd.edu/rammcap/cgi-bin/rammcap_2d.cgi | (208) |
| ProViDE | ProViDE is a tool for the analysis of viral diversity in metagenomic samples. | https://omictools.com/provide-tool | (209) |
| Phyloseq | Phyloseq is a tool-kit for raw reads pre-processing, diversity analysis and graphics production. It is an R, Bioconductor package. | https://joey711.github.io/phyloseq/ | (210) |
| Metagenome Seq | MetagenomeSeq is designed to determine the analysis of differential abundance of 16S rRNA gene in metaprofiling data. It is also designed to address the effects of both under-sampling and normalization of microbial communities on the basis of disease association detection. | http://bioconductor.org/packages/release/bioc/html/metagenomeSeq.html | (211) |
| Shotgun Functionalize R | Shotgun Functionalize is an R-Package for the functional assessment of metagenomic data. The package includes tools designed for importing, annotating and visualizing metagenomic data generated via high-throughput sequencing. | http://shotgun.math.chalmers.se/ | (212) |
| Galaxy portal | Galaxy portal is a web repository of computational tools that can be run without informatics expertise. It is a graphical interface and free service. | https://usegalaxy.org/ | (213) |
| MG-RAST | MG-RAST an open source web application is used for the automatic phylogenetic and functional analysis of metagenomes. MG-RAST is one of the biggest repositories for metagenomic data. It is a Graphical interface, web portal and free service. | http://metagenomics.anl.gov/ | (214) |
| IMG/M | IMG (Integrated Microbial Genomes) system serves as a community resource for the analysis, functional annotation and phylogenetic distribution of genes and comparative metagenomics. It is a graphical interface, web portal and free in service. | https://img.jgi.doe.gov/ | (215) |
| Phinch | Phinch is an open source, interactive exploratory data visualizing tool intended to alleviate the analysis of meta-omic datasets. The main features of this software are streamlined visualization workflow, sleek user interface, novel exploration of larger datasets. Accessible via web browser. | http://phinch.org | (215) |
| CAMERA | CAMERA is an important tool that aims to bridge the gaps and to develop methods so as to monitor microbial communities of the oceans. CAMERA's databases incorporate both the genomic and metagenomic datasets, metadata, results from the pre computed analysis and softwares that endorse commanding cross-analysis of the environmental metagenomes. | https://omictools.com/camera-2-tool | (216) |
| Meta Comp | Meta Comp is a graphical inclusive analysis tool that encompasses a series of statistical analysis approaches along with visualized results for comparative analysis of metagenomics as well as other meta-omics data sets. The software has the features to read files generated via different upstream analysis programs. It has also got the features to automatically choose two-group sample test. | http://cqb.pku.edu.cn/ZhuLab/MetaComp/ | (216) |