Table 3.
List of bioinformatics tools for studying the gut microbiome via methods including metagenomics and metatranscriptomics (all mentioned URLs were accessed on 28 November 2021).
| Method | Description | Tools | URL | Reference |
|---|---|---|---|---|
| Metagenomics | Metagenomics is the culture-independent analysis of a collection of genomes from microbial communities contained in natural living environments. | MetaPhlAn2 | https://huttenhower.sph.harvard.edu/metaphlan2/ | [110] |
| MG-RAST | https://www.mg-rast.org/ | [113] | ||
| MEGAHIT | https://github.com/voutcn/megahit | [114] | ||
| HUMAnN2 | https://huttenhower.sph.harvard.edu/humann2/ | [115] | ||
| QIIME | http://qiime.org/ | [116] | ||
| mothur | https://mothur.org/ | [117] | ||
| SPades | https://cab.spbu.ru/software/spades/ | [118] | ||
| Metatranscriptomics | Metatranscriptomics, also a culture-independent method, allows studying of the expressed RNA transcripts in the microbiome. | SOAPdenovo | http://soapdenovo2.sourceforge.net/ | [119] |
| SAMSA2 | https://github.com/transcript/samsa2 | [120] | ||
| mOTUs2 |
https://motu-tool.org/
https://github.com/motu-tool/mOTUs |
[121] |